data_2D2C
#
_model_server_result.job_id            lTffM0EXZ5NWFlR9xDRxBQ 
_model_server_result.datetime_utc      '2024-11-06 00:06:22' 
_model_server_result.server_version    0.9.12 
_model_server_result.query_name        ligand 
_model_server_result.source_id         pdb-bcif 
_model_server_result.entry_id          2d2c 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"R","auth_seq_id":302}' 
#
_entry.id    2D2C 
#
_exptl.entry_id    2D2C 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              616.487 
_entity.id                          9 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PROTOPORPHYRIN IX CONTAINING FE' 
_entity.pdbx_number_of_molecules    6 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         120 
_cell.entry_id            2D2C 
_cell.length_a            156.587 
_cell.length_b            156.587 
_cell.length_c            361.786 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2D2C 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        169 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 61' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexadecameric 
_pdbx_struct_assembly.oligomeric_count      16 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1 
#
_pdbx_struct_oper_list.id                    1 
_pdbx_struct_oper_list.type                  'identity operation' 
_pdbx_struct_oper_list.name                  1_555 
_pdbx_struct_oper_list.symmetry_operation    x,y,z 
_pdbx_struct_oper_list.matrix[1][1]          1 
_pdbx_struct_oper_list.matrix[1][2]          0 
_pdbx_struct_oper_list.matrix[1][3]          0 
_pdbx_struct_oper_list.matrix[2][1]          0 
_pdbx_struct_oper_list.matrix[2][2]          1 
_pdbx_struct_oper_list.matrix[2][3]          0 
_pdbx_struct_oper_list.matrix[3][1]          0 
_pdbx_struct_oper_list.matrix[3][2]          0 
_pdbx_struct_oper_list.matrix[3][3]          1 
_pdbx_struct_oper_list.vector[1]             0 
_pdbx_struct_oper_list.vector[2]             0 
_pdbx_struct_oper_list.vector[3]             0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 9 Q N N 
? 9 R N N 
? 9 X N N 
? 9 AA N N 
? 9 BA N N 
? 9 HA N N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
disulf ? disulf1 D SG CYS 113 D CYS 113 1_555 D SG CYS 128 D CYS 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.682 ? 
disulf ? disulf2 L SG CYS 113 Q CYS 113 1_555 L SG CYS 128 Q CYS 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.675 ? 
covale ? covale1 A SG CYS 35 A CYS 35 1_555 S CAB HEC . A HEC 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.789 ? 
covale ? covale2 C SG CYS 22 C CYS 22 1_555 X CAB HEM . C HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.844 ? 
covale ? covale3 C SG CYS 25 C CYS 25 1_555 X CAC HEM . C HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.869 ? 
covale ? covale4 I SG CYS 35 N CYS 35 1_555 CA CAB HEC . N HEC 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.804 ? 
covale ? covale5 K SG CYS 22 P CYS 22 1_555 HA CAB HEM . P HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.836 ? 
covale ? covale6 K SG CYS 25 P CYS 25 1_555 HA CAC HEM . P HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.822 ? 
metalc ? metalc1 A NE2 HIS 86 A HIS 86 1_555 Q FE HEM . A HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? 
metalc ? metalc2 A NE2 HIS 100 A HIS 100 1_555 R FE HEM . A HEM 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? 
metalc ? metalc3 A NE2 HIS 187 A HIS 187 1_555 Q FE HEM . A HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? 
metalc ? metalc4 A NE2 HIS 202 A HIS 202 1_555 R FE HEM . A HEM 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? 
metalc ? metalc5 S FE HEC . A HEC 303 1_555 KA O HOH . A HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.529 ? 
metalc ? metalc6 C N TYR 1 C TYR 1 1_555 X FE HEM . C HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? 
metalc ? metalc7 D SG CYS 108 D CYS 108 1_555 Y FE1 FES . D FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? 
metalc ? metalc8 D ND1 HIS 110 D HIS 110 1_555 Y FE2 FES . D FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.58 ? 
metalc ? metalc9 D SG CYS 126 D CYS 126 1_555 Y FE1 FES . D FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? 
metalc ? metalc10 D ND1 HIS 129 D HIS 129 1_555 Y FE2 FES . D FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? 
metalc ? metalc11 I NE2 HIS 86 N HIS 86 1_555 AA FE HEM . N HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? 
metalc ? metalc12 I NE2 HIS 100 N HIS 100 1_555 BA FE HEM . N HEM 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? 
metalc ? metalc13 I NE2 HIS 187 N HIS 187 1_555 AA FE HEM . N HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? 
metalc ? metalc14 I NE2 HIS 202 N HIS 202 1_555 BA FE HEM . N HEM 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? 
metalc ? metalc15 CA FE HEC . N HEC 303 1_555 LA O HOH . N HOH 1306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? 
metalc ? metalc16 K N TYR 1 P TYR 1 1_555 HA FE HEM . P HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? 
metalc ? metalc17 L SG CYS 108 Q CYS 108 1_555 IA FE1 FES . Q FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.539 ? 
metalc ? metalc18 L ND1 HIS 110 Q HIS 110 1_555 IA FE2 FES . Q FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? 
metalc ? metalc19 L SG CYS 126 Q CYS 126 1_555 IA FE1 FES . Q FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? 
metalc ? metalc20 L ND1 HIS 129 Q HIS 129 1_555 IA FE2 FES . Q FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? 
#
_chem_comp.formula           'C34 H32 Fe N4 O4' 
_chem_comp.formula_weight    616.487 
_chem_comp.id                HEM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'PROTOPORPHYRIN IX CONTAINING FE' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     HEME 
#
loop_
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.comp_id
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_ordinal
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_aromatic_flag
CHA C1A HEM sing 483 n n 
CHA C4D HEM doub 484 n n 
CHA HHA HEM sing 485 n n 
CHB C4A HEM sing 486 n n 
CHB C1B HEM doub 487 n n 
CHB HHB HEM sing 488 n n 
CHC C4B HEM sing 489 n n 
CHC C1C HEM doub 490 n n 
CHC HHC HEM sing 491 n n 
CHD C4C HEM doub 492 n n 
CHD C1D HEM sing 493 n n 
CHD HHD HEM sing 494 n n 
C1A C2A HEM doub 495 n y 
C1A NA HEM sing 496 n y 
C2A C3A HEM sing 497 n y 
C2A CAA HEM sing 498 n n 
C3A C4A HEM doub 499 n y 
C3A CMA HEM sing 500 n n 
C4A NA HEM sing 501 n y 
CMA HMA HEM sing 502 n n 
CMA HMAA HEM sing 503 n n 
CMA HMAB HEM sing 504 n n 
CAA CBA HEM sing 505 n n 
CAA HAA HEM sing 506 n n 
CAA HAAA HEM sing 507 n n 
CBA CGA HEM sing 508 n n 
CBA HBA HEM sing 509 n n 
CBA HBAA HEM sing 510 n n 
CGA O1A HEM doub 511 n n 
CGA O2A HEM sing 512 n n 
C1B C2B HEM sing 513 n n 
C1B NB HEM sing 514 n n 
C2B C3B HEM doub 515 n n 
C2B CMB HEM sing 516 n n 
C3B C4B HEM sing 517 n n 
C3B CAB HEM sing 518 n n 
C4B NB HEM doub 519 n n 
CMB HMB HEM sing 520 n n 
CMB HMBA HEM sing 521 n n 
CMB HMBB HEM sing 522 n n 
CAB CBB HEM doub 523 n n 
CAB HAB HEM sing 524 n n 
CBB HBB HEM sing 525 n n 
CBB HBBA HEM sing 526 n n 
C1C C2C HEM sing 527 n y 
C1C NC HEM sing 528 n y 
C2C C3C HEM doub 529 n y 
C2C CMC HEM sing 530 n n 
C3C C4C HEM sing 531 n y 
C3C CAC HEM sing 532 n n 
C4C NC HEM sing 533 n y 
CMC HMC HEM sing 534 n n 
CMC HMCA HEM sing 535 n n 
CMC HMCB HEM sing 536 n n 
CAC CBC HEM doub 537 n n 
CAC HAC HEM sing 538 n n 
CBC HBC HEM sing 539 n n 
CBC HBCA HEM sing 540 n n 
C1D C2D HEM sing 541 n n 
C1D ND HEM doub 542 n n 
C2D C3D HEM doub 543 n n 
C2D CMD HEM sing 544 n n 
C3D C4D HEM sing 545 n n 
C3D CAD HEM sing 546 n n 
C4D ND HEM sing 547 n n 
CMD HMD HEM sing 548 n n 
CMD HMDA HEM sing 549 n n 
CMD HMDB HEM sing 550 n n 
CAD CBD HEM sing 551 n n 
CAD HAD HEM sing 552 n n 
CAD HADA HEM sing 553 n n 
CBD CGD HEM sing 554 n n 
CBD HBD HEM sing 555 n n 
CBD HBDA HEM sing 556 n n 
CGD O1D HEM doub 557 n n 
CGD O2D HEM sing 558 n n 
O2A H2A HEM sing 559 n n 
O2D H2D HEM sing 560 n n 
FE NA HEM sing 561 n n 
FE NB HEM sing 562 n n 
FE NC HEM sing 563 n n 
FE ND HEM sing 564 n n 
#
_atom_sites.entry_id                     2D2C 
_atom_sites.fract_transf_matrix[1][1]    0.006386 
_atom_sites.fract_transf_matrix[1][2]    0.003687 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007374 
_atom_sites.fract_transf_matrix[2][3]    0 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.002764 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_ins_code
Q 9 HEM A 1 301 301 HEM HEM . 
R 9 HEM A 1 302 302 HEM HEM . 
S 10 HEC A 1 303 303 HEC HEC . 
T 11 OPC B 1 305 305 OPC OPC . 
U 12 BNT B 1 309 309 BNT DBM . 
V 13 CLA B 1 201 201 CLA CLA . 
W 11 OPC C 1 306 306 OPC OPC . 
X 9 HEM C 1 301 301 HEM HEM . 
Y 14 FES D 1 201 201 FES FES . 
Z 15 BCR E 1 101 101 BCR BCR . 
AA 9 HEM N 1 301 301 HEM HEM . 
BA 9 HEM N 1 302 302 HEM HEM . 
CA 10 HEC N 1 303 303 HEC HEC . 
DA 11 OPC N 1 1305 305 OPC OPC . 
EA 11 OPC O 1 1306 306 OPC OPC . 
FA 12 BNT O 1 1309 309 BNT DBM . 
GA 13 CLA O 1 1201 201 CLA CLA . 
HA 9 HEM P 1 301 301 HEM HEM . 
IA 14 FES Q 1 201 201 FES FES . 
JA 15 BCR R 1 1101 101 BCR BCR . 
KA 16 HOH A 1 304 2 HOH HOH . 
LA 16 HOH N 1 1306 1 HOH HOH . 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1 C CHA HEM . . . R 9 81.659 15.389 79.695 1 58.14 ? CHA HEM 302 A 1 
HETATM 2 C CHB HEM . . . R 9 79.966 11.053 80.988 1 58.14 ? CHB HEM 302 A 1 
HETATM 3 C CHC HEM . . . R 9 84.118 9.006 79.87 1 58.14 ? CHC HEM 302 A 1 
HETATM 4 C CHD HEM . . . R 9 85.882 13.312 78.593 1 58.14 ? CHD HEM 302 A 1 
HETATM 5 C C1A HEM . . . R 9 80.805 14.382 80.146 1 58.14 ? C1A HEM 302 A 1 
HETATM 6 C C2A HEM . . . R 9 79.367 14.491 80.519 1 58.14 ? C2A HEM 302 A 1 
HETATM 7 C C3A HEM . . . R 9 78.948 13.296 80.89 1 58.14 ? C3A HEM 302 A 1 
HETATM 8 C C4A HEM . . . R 9 80.05 12.373 80.74 1 58.14 ? C4A HEM 302 A 1 
HETATM 9 C CMA HEM . . . R 9 77.597 12.7 81.381 1 58.14 ? CMA HEM 302 A 1 
HETATM 10 C CAA HEM . . . R 9 78.621 15.752 80.405 1 58.14 ? CAA HEM 302 A 1 
HETATM 11 C CBA HEM . . . R 9 78.038 15.294 79.039 1 58.14 ? CBA HEM 302 A 1 
HETATM 12 C CGA HEM . . . R 9 77.084 16.018 78.208 1 58.14 ? CGA HEM 302 A 1 
HETATM 13 O O1A HEM . . . R 9 77.488 16.915 77.468 1 58.14 ? O1A HEM 302 A 1 
HETATM 14 O O2A HEM . . . R 9 75.791 15.545 78.276 1 58.14 ? O2A HEM 302 A 1 
HETATM 15 C C1B HEM . . . R 9 80.928 10.145 80.813 1 58.14 ? C1B HEM 302 A 1 
HETATM 16 C C2B HEM . . . R 9 80.761 8.747 81.079 1 58.14 ? C2B HEM 302 A 1 
HETATM 17 C C3B HEM . . . R 9 81.943 8.151 80.76 1 58.14 ? C3B HEM 302 A 1 
HETATM 18 C C4B HEM . . . R 9 82.825 9.19 80.3 1 58.14 ? C4B HEM 302 A 1 
HETATM 19 C CMB HEM . . . R 9 79.481 8.128 81.6 1 58.14 ? CMB HEM 302 A 1 
HETATM 20 C CAB HEM . . . R 9 82.062 6.694 80.927 1 58.14 ? CAB HEM 302 A 1 
HETATM 21 C CBB HEM . . . R 9 82.921 6.019 81.733 1 58.14 ? CBB HEM 302 A 1 
HETATM 22 C C1C HEM . . . R 9 84.971 9.985 79.415 1 58.14 ? C1C HEM 302 A 1 
HETATM 23 C C2C HEM . . . R 9 86.388 9.734 78.897 1 58.14 ? C2C HEM 302 A 1 
HETATM 24 C C3C HEM . . . R 9 86.873 10.934 78.544 1 58.14 ? C3C HEM 302 A 1 
HETATM 25 C C4C HEM . . . R 9 85.784 11.965 78.825 1 58.14 ? C4C HEM 302 A 1 
HETATM 26 C CMC HEM . . . R 9 87.039 8.377 78.82 1 58.14 ? CMC HEM 302 A 1 
HETATM 27 C CAC HEM . . . R 9 88.246 11.235 77.952 1 58.14 ? CAC HEM 302 A 1 
HETATM 28 C CBC HEM . . . R 9 88.551 11.07 76.661 1 58.14 ? CBC HEM 302 A 1 
HETATM 29 C C1D HEM . . . R 9 84.893 14.27 78.798 1 58.14 ? C1D HEM 302 A 1 
HETATM 30 C C2D HEM . . . R 9 85.059 15.656 78.532 1 58.14 ? C2D HEM 302 A 1 
HETATM 31 C C3D HEM . . . R 9 83.879 16.291 78.825 1 58.14 ? C3D HEM 302 A 1 
HETATM 32 C C4D HEM . . . R 9 82.983 15.206 79.292 1 58.14 ? C4D HEM 302 A 1 
HETATM 33 C CMD HEM . . . R 9 86.354 16.278 77.997 1 58.14 ? CMD HEM 302 A 1 
HETATM 34 C CAD HEM . . . R 9 83.414 17.673 78.756 1 58.14 ? CAD HEM 302 A 1 
HETATM 35 C CBD HEM . . . R 9 83.69 18.284 77.349 1 58.14 ? CBD HEM 302 A 1 
HETATM 36 C CGD HEM . . . R 9 83.24 19.738 77.254 1 58.14 ? CGD HEM 302 A 1 
HETATM 37 O O1D HEM . . . R 9 82.861 20.18 76.125 1 58.14 ? O1D HEM 302 A 1 
HETATM 38 O O2D HEM . . . R 9 83.295 20.431 78.321 1 58.14 ? O2D HEM 302 A 1 
HETATM 39 N NA HEM . . . R 9 81.143 13.057 80.282 1 58.14 ? NA HEM 302 A 1 
HETATM 40 N NB HEM . . . R 9 82.174 10.406 80.349 1 58.14 ? NB HEM 302 A 1 
HETATM 41 N NC HEM . . . R 9 84.687 11.331 79.331 1 58.14 ? NC HEM 302 A 1 
HETATM 42 N ND HEM . . . R 9 83.656 14.043 79.263 1 58.14 ? ND HEM 302 A 1 
HETATM 43 FE FE HEM . . . R 9 82.916 12.252 79.844 1 41.75 ? FE HEM 302 A 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    65 
_model_server_stats.query_time_ms           319 
_model_server_stats.encode_time_ms          13 
_model_server_stats.element_count           43 
#