data_2DGL
#
_model_server_result.job_id            rLq5Q4ZMophpN9Xj1RwCXQ 
_model_server_result.datetime_utc      '2024-11-27 04:14:50' 
_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          2dgl 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"X","auth_seq_id":501}' 
#
_entry.id    2DGL 
#
_exptl.entry_id    2DGL 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              247.142 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "PYRIDOXAL-5'-PHOSPHATE" 
_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            2DGL 
_cell.length_a            297.051 
_cell.length_b            297.051 
_cell.length_c            233.731 
_cell.Z_PDB               72 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2DGL 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        182 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 63 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA 
_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
? 3 K N N 
? 3 R N N 
? 3 X N N 
? 3 DA N N 
? 3 IA N N 
? 3 OA 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
covale ? covale1 A NZ LYS 276 A LYS 276 1_555 K C4A PLP . A PLP 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? 
covale ? covale2 B NZ LYS 276 B LYS 276 1_555 R C4A PLP . B PLP 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? 
covale ? covale3 C NZ LYS 276 C LYS 276 1_555 X C4A PLP . C PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? 
covale ? covale4 D NZ LYS 276 D LYS 276 1_555 DA C4A PLP . D PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? 
covale ? covale5 E NZ LYS 276 E LYS 276 1_555 IA C4A PLP . E PLP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.316 ? 
covale ? covale6 F NZ LYS 276 F LYS 276 1_555 OA C4A PLP . F PLP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? 
#
_chem_comp.formula           'C8 H10 N O6 P' 
_chem_comp.formula_weight    247.142 
_chem_comp.id                PLP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "PYRIDOXAL-5'-PHOSPHATE" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'VITAMIN B6 Phosphate' 
#
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
N1 C2 PLP doub 267 n y 
N1 C6 PLP sing 268 n y 
C2 C2A PLP sing 269 n n 
C2 C3 PLP sing 270 n y 
C2A H2A1 PLP sing 271 n n 
C2A H2A2 PLP sing 272 n n 
C2A H2A3 PLP sing 273 n n 
C3 O3 PLP sing 274 n n 
C3 C4 PLP doub 275 n y 
O3 HO3 PLP sing 276 n n 
C4 C4A PLP sing 277 n n 
C4 C5 PLP sing 278 n y 
C4A O4A PLP doub 279 n n 
C4A H4A PLP sing 280 n n 
C5 C6 PLP doub 281 n y 
C5 C5A PLP sing 282 n n 
C6 H6 PLP sing 283 n n 
C5A O4P PLP sing 284 n n 
C5A H5A1 PLP sing 285 n n 
C5A H5A2 PLP sing 286 n n 
O4P P PLP sing 287 n n 
P O1P PLP doub 288 n n 
P O2P PLP sing 289 n n 
P O3P PLP sing 290 n n 
O2P HOP2 PLP sing 291 n n 
O3P HOP3 PLP sing 292 n n 
#
_atom_sites.entry_id                     2DGL 
_atom_sites.fract_transf_matrix[1][1]    0.003366 
_atom_sites.fract_transf_matrix[1][2]    0.001944 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.003887 
_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]    0.004278 
_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
G 2 BR A 1 467 301 BR BR . 
H 2 BR A 1 468 303 BR BR . 
I 2 BR A 1 469 317 BR BR . 
J 2 BR A 1 470 319 BR BR . 
K 3 PLP A 1 500 500 PLP PLP . 
L 4 ACY A 1 568 518 ACY ACY . 
M 2 BR B 1 467 304 BR BR . 
N 2 BR B 1 468 306 BR BR . 
O 2 BR B 1 469 307 BR BR . 
P 2 BR B 1 470 308 BR BR . 
Q 2 BR B 1 471 320 BR BR . 
R 3 PLP B 1 500 500 PLP PLP . 
S 4 ACY B 1 558 518 ACY ACY . 
T 2 BR C 1 467 305 BR BR . 
U 2 BR C 1 468 309 BR BR . 
V 2 BR C 1 469 314 BR BR . 
W 2 BR C 1 470 321 BR BR . 
X 3 PLP C 1 501 501 PLP PLP . 
Y 4 ACY C 1 538 518 ACY ACY . 
Z 4 ACY C 1 548 518 ACY ACY . 
AA 2 BR D 1 467 310 BR BR . 
BA 2 BR D 1 468 312 BR BR . 
CA 2 BR D 1 469 322 BR BR . 
DA 3 PLP D 1 501 501 PLP PLP . 
EA 2 BR E 1 467 311 BR BR . 
FA 2 BR E 1 468 313 BR BR . 
GA 2 BR E 1 469 315 BR BR . 
HA 2 BR E 1 470 323 BR BR . 
IA 3 PLP E 1 502 502 PLP PLP . 
JA 4 ACY E 1 518 518 ACY ACY . 
KA 2 BR F 1 467 302 BR BR . 
LA 2 BR F 1 468 316 BR BR . 
MA 2 BR F 1 469 318 BR BR . 
NA 2 BR F 1 470 324 BR BR . 
OA 3 PLP F 1 502 502 PLP PLP . 
PA 4 ACY F 1 528 518 ACY ACY . 
QA 5 HOH A 1 569 1 HOH HOH . 
QA 5 HOH A 2 570 4 HOH HOH . 
QA 5 HOH A 3 571 5 HOH HOH . 
QA 5 HOH A 4 572 6 HOH HOH . 
QA 5 HOH A 5 573 8 HOH HOH . 
QA 5 HOH A 6 574 9 HOH HOH . 
QA 5 HOH A 7 575 10 HOH HOH . 
QA 5 HOH A 8 576 11 HOH HOH . 
QA 5 HOH A 9 577 12 HOH HOH . 
QA 5 HOH A 10 578 13 HOH HOH . 
QA 5 HOH A 11 579 14 HOH HOH . 
QA 5 HOH A 12 580 15 HOH HOH . 
QA 5 HOH A 13 581 16 HOH HOH . 
QA 5 HOH A 14 582 19 HOH HOH . 
QA 5 HOH A 15 583 27 HOH HOH . 
QA 5 HOH A 16 584 28 HOH HOH . 
QA 5 HOH A 17 585 91 HOH HOH . 
QA 5 HOH A 18 586 107 HOH HOH . 
QA 5 HOH A 19 587 110 HOH HOH . 
QA 5 HOH A 20 588 115 HOH HOH . 
QA 5 HOH A 21 589 117 HOH HOH . 
QA 5 HOH A 22 590 120 HOH HOH . 
QA 5 HOH A 23 591 126 HOH HOH . 
RA 5 HOH B 1 559 2 HOH HOH . 
RA 5 HOH B 2 560 7 HOH HOH . 
RA 5 HOH B 3 561 17 HOH HOH . 
RA 5 HOH B 4 562 18 HOH HOH . 
RA 5 HOH B 5 563 20 HOH HOH . 
RA 5 HOH B 6 564 21 HOH HOH . 
RA 5 HOH B 7 565 23 HOH HOH . 
RA 5 HOH B 8 566 24 HOH HOH . 
RA 5 HOH B 9 567 25 HOH HOH . 
RA 5 HOH B 10 568 26 HOH HOH . 
RA 5 HOH B 11 569 29 HOH HOH . 
RA 5 HOH B 12 570 30 HOH HOH . 
RA 5 HOH B 13 571 31 HOH HOH . 
RA 5 HOH B 14 572 32 HOH HOH . 
RA 5 HOH B 15 573 33 HOH HOH . 
RA 5 HOH B 16 574 34 HOH HOH . 
RA 5 HOH B 17 575 35 HOH HOH . 
RA 5 HOH B 18 576 36 HOH HOH . 
RA 5 HOH B 19 577 37 HOH HOH . 
RA 5 HOH B 20 578 38 HOH HOH . 
RA 5 HOH B 21 579 39 HOH HOH . 
RA 5 HOH B 22 580 40 HOH HOH . 
RA 5 HOH B 23 581 82 HOH HOH . 
RA 5 HOH B 24 582 85 HOH HOH . 
RA 5 HOH B 25 583 92 HOH HOH . 
RA 5 HOH B 26 584 93 HOH HOH . 
RA 5 HOH B 27 585 94 HOH HOH . 
RA 5 HOH B 28 586 95 HOH HOH . 
RA 5 HOH B 29 587 116 HOH HOH . 
RA 5 HOH B 30 588 119 HOH HOH . 
RA 5 HOH B 31 589 121 HOH HOH . 
RA 5 HOH B 32 590 123 HOH HOH . 
RA 5 HOH B 33 591 130 HOH HOH . 
SA 5 HOH C 1 549 22 HOH HOH . 
SA 5 HOH C 2 550 41 HOH HOH . 
SA 5 HOH C 3 551 43 HOH HOH . 
SA 5 HOH C 4 552 44 HOH HOH . 
SA 5 HOH C 5 553 45 HOH HOH . 
SA 5 HOH C 6 554 46 HOH HOH . 
SA 5 HOH C 7 555 47 HOH HOH . 
SA 5 HOH C 8 556 48 HOH HOH . 
SA 5 HOH C 9 557 99 HOH HOH . 
SA 5 HOH C 10 558 101 HOH HOH . 
SA 5 HOH C 11 559 102 HOH HOH . 
SA 5 HOH C 12 560 103 HOH HOH . 
SA 5 HOH C 13 561 111 HOH HOH . 
SA 5 HOH C 14 562 118 HOH HOH . 
TA 5 HOH D 1 502 49 HOH HOH . 
TA 5 HOH D 2 503 50 HOH HOH . 
TA 5 HOH D 3 504 51 HOH HOH . 
TA 5 HOH D 4 505 52 HOH HOH . 
TA 5 HOH D 5 506 53 HOH HOH . 
TA 5 HOH D 6 507 54 HOH HOH . 
TA 5 HOH D 7 508 84 HOH HOH . 
TA 5 HOH D 8 509 105 HOH HOH . 
TA 5 HOH D 9 510 109 HOH HOH . 
TA 5 HOH D 10 511 125 HOH HOH . 
TA 5 HOH D 11 512 129 HOH HOH . 
TA 5 HOH D 12 513 131 HOH HOH . 
TA 5 HOH D 13 514 132 HOH HOH . 
UA 5 HOH E 1 519 42 HOH HOH . 
UA 5 HOH E 2 520 55 HOH HOH . 
UA 5 HOH E 3 521 58 HOH HOH . 
UA 5 HOH E 4 522 59 HOH HOH . 
UA 5 HOH E 5 523 60 HOH HOH . 
UA 5 HOH E 6 524 61 HOH HOH . 
UA 5 HOH E 7 525 62 HOH HOH . 
UA 5 HOH E 8 526 63 HOH HOH . 
UA 5 HOH E 9 527 64 HOH HOH . 
UA 5 HOH E 10 528 65 HOH HOH . 
UA 5 HOH E 11 529 66 HOH HOH . 
UA 5 HOH E 12 530 68 HOH HOH . 
UA 5 HOH E 13 531 69 HOH HOH . 
UA 5 HOH E 14 532 70 HOH HOH . 
UA 5 HOH E 15 533 76 HOH HOH . 
UA 5 HOH E 16 534 81 HOH HOH . 
UA 5 HOH E 17 535 86 HOH HOH . 
UA 5 HOH E 18 536 89 HOH HOH . 
UA 5 HOH E 19 537 98 HOH HOH . 
UA 5 HOH E 20 538 106 HOH HOH . 
UA 5 HOH E 21 539 108 HOH HOH . 
UA 5 HOH E 22 540 112 HOH HOH . 
UA 5 HOH E 23 541 122 HOH HOH . 
UA 5 HOH E 24 542 128 HOH HOH . 
UA 5 HOH E 25 543 133 HOH HOH . 
UA 5 HOH E 26 544 134 HOH HOH . 
VA 5 HOH F 1 529 3 HOH HOH . 
VA 5 HOH F 2 530 56 HOH HOH . 
VA 5 HOH F 3 531 57 HOH HOH . 
VA 5 HOH F 4 532 67 HOH HOH . 
VA 5 HOH F 5 533 71 HOH HOH . 
VA 5 HOH F 6 534 72 HOH HOH . 
VA 5 HOH F 7 535 73 HOH HOH . 
VA 5 HOH F 8 536 74 HOH HOH . 
VA 5 HOH F 9 537 75 HOH HOH . 
VA 5 HOH F 10 538 77 HOH HOH . 
VA 5 HOH F 11 539 78 HOH HOH . 
VA 5 HOH F 12 540 79 HOH HOH . 
VA 5 HOH F 13 541 80 HOH HOH . 
VA 5 HOH F 14 542 83 HOH HOH . 
VA 5 HOH F 15 543 87 HOH HOH . 
VA 5 HOH F 16 544 88 HOH HOH . 
VA 5 HOH F 17 545 90 HOH HOH . 
VA 5 HOH F 18 546 96 HOH HOH . 
VA 5 HOH F 19 547 97 HOH HOH . 
VA 5 HOH F 20 548 100 HOH HOH . 
VA 5 HOH F 21 549 104 HOH HOH . 
VA 5 HOH F 22 550 113 HOH HOH . 
VA 5 HOH F 23 551 114 HOH HOH . 
VA 5 HOH F 24 552 124 HOH HOH . 
VA 5 HOH F 25 553 127 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 N N1 PLP . . . X 3 -62.222 53.629 -34.143 1 43.55 ? N1 PLP 501 C 1 
HETATM 2 C C2 PLP . . . X 3 -62.868 53.327 -32.999 1 43.57 ? C2 PLP 501 C 1 
HETATM 3 C C2A PLP . . . X 3 -62.228 52.36 -32.05 1 44.47 ? C2A PLP 501 C 1 
HETATM 4 C C3 PLP . . . X 3 -64.125 53.942 -32.771 1 43.84 ? C3 PLP 501 C 1 
HETATM 5 O O3 PLP . . . X 3 -64.825 53.701 -31.641 1 43.28 ? O3 PLP 501 C 1 
HETATM 6 C C4 PLP . . . X 3 -64.655 54.844 -33.747 1 44.35 ? C4 PLP 501 C 1 
HETATM 7 C C4A PLP . . . X 3 -66.014 55.494 -33.46 1 45.49 ? C4A PLP 501 C 1 
HETATM 8 C C5 PLP . . . X 3 -63.905 55.095 -34.927 1 44.2 ? C5 PLP 501 C 1 
HETATM 9 C C6 PLP . . . X 3 -62.697 54.474 -35.081 1 43.73 ? C6 PLP 501 C 1 
HETATM 10 C C5A PLP . . . X 3 -64.411 55.987 -36.067 1 43.82 ? C5A PLP 501 C 1 
HETATM 11 O O4P PLP . . . X 3 -63.89 57.311 -35.905 1 42.44 ? O4P PLP 501 C 1 
HETATM 12 P P PLP . . . X 3 -64.853 58.531 -36.297 1 39.36 ? P PLP 501 C 1 
HETATM 13 O O1P PLP . . . X 3 -64.571 58.863 -37.735 1 36.96 ? O1P PLP 501 C 1 
HETATM 14 O O2P PLP . . . X 3 -64.402 59.72 -35.403 1 39.31 ? O2P PLP 501 C 1 
HETATM 15 O O3P PLP . . . X 3 -66.241 58.119 -35.898 1 38.56 ? O3P PLP 501 C 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    27 
_model_server_stats.query_time_ms           277 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           15 
#