data_4XF6
#
_model_server_result.job_id            J2aLTGeMOw2V2FmNxmPBPw 
_model_server_result.datetime_utc      '2024-11-24 14:31:14' 
_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          4xf6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":302}' 
#
_entry.id    4XF6 
#
_exptl.entry_id    4XF6 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    2 
_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         90 
_cell.entry_id            4XF6 
_cell.length_a            77.364 
_cell.length_b            81.255 
_cell.length_c            82.046 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4XF6 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,AA 1 1 
B,S,T,U,V,W,X,Y,Z,BA 2 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 D N N 
? 3 T 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 G I IOD . A IOD 305 1_555 L I IOD . A IOD 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.098 ? 
metalc ? metalc1 A OE1 GLN 136 A GLN 136 1_555 F MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? 
metalc ? metalc2 C O8 LIP . A LIP 301 1_555 F MG MG . A MG 304 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.045 ? 
metalc ? metalc3 D O3B ADP . A ADP 302 1_555 F MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? 
metalc ? metalc4 F MG MG . A MG 304 1_555 AA O HOH . A HOH 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? 
metalc ? metalc5 F MG MG . A MG 304 1_555 AA O HOH . A HOH 417 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? 
metalc ? metalc6 F MG MG . A MG 304 1_555 AA O HOH . A HOH 422 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
metalc ? metalc7 B OE1 GLN 136 B GLN 136 1_555 V MG MG . B MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? 
metalc ? metalc8 S O7 LIP . B LIP 301 1_555 V MG MG . B MG 304 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.071 ? 
metalc ? metalc9 T O1B ADP . B ADP 302 1_555 V MG MG . B MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
metalc ? metalc10 V MG MG . B MG 304 1_555 BA O HOH . B HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? 
metalc ? metalc11 V MG MG . B MG 304 1_555 BA O HOH . B HOH 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? 
metalc ? metalc12 V MG MG . B MG 304 1_555 BA O HOH . B HOH 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? 
#
_chem_comp.formula           'C10 H15 N5 O10 P2' 
_chem_comp.formula_weight    427.201 
_chem_comp.id                ADP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "ADENOSINE-5'-DIPHOSPHATE" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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
PB O1B ADP doub 1 n n 
PB O2B ADP sing 2 n n 
PB O3B ADP sing 3 n n 
PB O3A ADP sing 4 n n 
O2B HOB2 ADP sing 5 n n 
O3B HOB3 ADP sing 6 n n 
PA O1A ADP doub 7 n n 
PA O2A ADP sing 8 n n 
PA O3A ADP sing 9 n n 
PA O5' ADP sing 10 n n 
O2A HOA2 ADP sing 11 n n 
O5' C5' ADP sing 12 n n 
C5' C4' ADP sing 13 n n 
C5' "H5'1" ADP sing 14 n n 
C5' "H5'2" ADP sing 15 n n 
C4' O4' ADP sing 16 n n 
C4' C3' ADP sing 17 n n 
C4' H4' ADP sing 18 n n 
O4' C1' ADP sing 19 n n 
C3' O3' ADP sing 20 n n 
C3' C2' ADP sing 21 n n 
C3' H3' ADP sing 22 n n 
O3' HO3' ADP sing 23 n n 
C2' O2' ADP sing 24 n n 
C2' C1' ADP sing 25 n n 
C2' H2' ADP sing 26 n n 
O2' HO2' ADP sing 27 n n 
C1' N9 ADP sing 28 n n 
C1' H1' ADP sing 29 n n 
N9 C8 ADP sing 30 n y 
N9 C4 ADP sing 31 n y 
C8 N7 ADP doub 32 n y 
C8 H8 ADP sing 33 n n 
N7 C5 ADP sing 34 n y 
C5 C6 ADP sing 35 n y 
C5 C4 ADP doub 36 n y 
C6 N6 ADP sing 37 n n 
C6 N1 ADP doub 38 n y 
N6 HN61 ADP sing 39 n n 
N6 HN62 ADP sing 40 n n 
N1 C2 ADP sing 41 n y 
C2 N3 ADP doub 42 n y 
C2 H2 ADP sing 43 n n 
N3 C4 ADP sing 44 n y 
#
_atom_sites.entry_id                     4XF6 
_atom_sites.fract_transf_matrix[1][1]    0.012926 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012307 
_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]    0.012188 
_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
C 2 LIP A 1 301 301 LIP MIP . 
D 3 ADP A 1 302 302 ADP ADP . 
E 4 INS A 1 303 303 INS INS . 
F 5 MG A 1 304 401 MG MG . 
G 6 IOD A 1 305 502 IOD IOD . 
H 6 IOD A 1 306 503 IOD IOD . 
I 6 IOD A 1 307 504 IOD IOD . 
J 6 IOD A 1 308 505 IOD IOD . 
K 6 IOD A 1 309 506 IOD IOD . 
L 6 IOD A 1 310 507 IOD IOD . 
M 6 IOD A 1 311 509 IOD IOD . 
N 6 IOD A 1 312 510 IOD IOD . 
O 6 IOD A 1 313 511 IOD IOD . 
P 6 IOD A 1 314 513 IOD IOD . 
Q 6 IOD A 1 315 515 IOD IOD . 
R 7 EDO A 1 316 701 EDO EDO . 
S 2 LIP B 1 301 301 LIP MIP . 
T 3 ADP B 1 302 302 ADP ADP . 
U 4 INS B 1 303 303 INS INS . 
V 5 MG B 1 304 401 MG MG . 
W 6 IOD B 1 305 501 IOD IOD . 
X 6 IOD B 1 306 508 IOD IOD . 
Y 6 IOD B 1 307 512 IOD IOD . 
Z 6 IOD B 1 308 514 IOD IOD . 
AA 8 HOH A 1 401 649 HOH HOH . 
AA 8 HOH A 2 402 612 HOH HOH . 
AA 8 HOH A 3 403 628 HOH HOH . 
AA 8 HOH A 4 404 615 HOH HOH . 
AA 8 HOH A 5 405 625 HOH HOH . 
AA 8 HOH A 6 406 643 HOH HOH . 
AA 8 HOH A 7 407 630 HOH HOH . 
AA 8 HOH A 8 408 622 HOH HOH . 
AA 8 HOH A 9 409 651 HOH HOH . 
AA 8 HOH A 10 410 659 HOH HOH . 
AA 8 HOH A 11 411 627 HOH HOH . 
AA 8 HOH A 12 412 648 HOH HOH . 
AA 8 HOH A 13 413 604 HOH HOH . 
AA 8 HOH A 14 414 605 HOH HOH . 
AA 8 HOH A 15 415 606 HOH HOH . 
AA 8 HOH A 16 416 607 HOH HOH . 
AA 8 HOH A 17 417 609 HOH HOH . 
AA 8 HOH A 18 418 611 HOH HOH . 
AA 8 HOH A 19 419 614 HOH HOH . 
AA 8 HOH A 20 420 616 HOH HOH . 
AA 8 HOH A 21 421 618 HOH HOH . 
AA 8 HOH A 22 422 619 HOH HOH . 
AA 8 HOH A 23 423 621 HOH HOH . 
AA 8 HOH A 24 424 623 HOH HOH . 
AA 8 HOH A 25 425 626 HOH HOH . 
AA 8 HOH A 26 426 629 HOH HOH . 
AA 8 HOH A 27 427 631 HOH HOH . 
AA 8 HOH A 28 428 633 HOH HOH . 
AA 8 HOH A 29 429 634 HOH HOH . 
AA 8 HOH A 30 430 637 HOH HOH . 
AA 8 HOH A 31 431 639 HOH HOH . 
AA 8 HOH A 32 432 641 HOH HOH . 
AA 8 HOH A 33 433 644 HOH HOH . 
AA 8 HOH A 34 434 646 HOH HOH . 
AA 8 HOH A 35 435 647 HOH HOH . 
AA 8 HOH A 36 436 650 HOH HOH . 
AA 8 HOH A 37 437 652 HOH HOH . 
BA 8 HOH B 1 401 658 HOH HOH . 
BA 8 HOH B 2 402 624 HOH HOH . 
BA 8 HOH B 3 403 613 HOH HOH . 
BA 8 HOH B 4 404 645 HOH HOH . 
BA 8 HOH B 5 405 653 HOH HOH . 
BA 8 HOH B 6 406 601 HOH HOH . 
BA 8 HOH B 7 407 602 HOH HOH . 
BA 8 HOH B 8 408 603 HOH HOH . 
BA 8 HOH B 9 409 608 HOH HOH . 
BA 8 HOH B 10 410 610 HOH HOH . 
BA 8 HOH B 11 411 617 HOH HOH . 
BA 8 HOH B 12 412 620 HOH HOH . 
BA 8 HOH B 13 413 632 HOH HOH . 
BA 8 HOH B 14 414 635 HOH HOH . 
BA 8 HOH B 15 415 636 HOH HOH . 
BA 8 HOH B 16 416 638 HOH HOH . 
BA 8 HOH B 17 417 640 HOH HOH . 
BA 8 HOH B 18 418 642 HOH HOH . 
BA 8 HOH B 19 419 654 HOH HOH . 
BA 8 HOH B 20 420 655 HOH HOH . 
BA 8 HOH B 21 421 656 HOH HOH . 
BA 8 HOH B 22 422 657 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 P PB ADP . . . D 3 11.536 80.984 0.712 1 31.84 ? PB ADP 302 A 1 
HETATM 2 O O1B ADP . . . D 3 12.632 80.482 -0.23 1 30.96 ? O1B ADP 302 A 1 
HETATM 3 O O2B ADP . . . D 3 10.214 81.108 -0.037 1 35.89 ? O2B ADP 302 A 1 
HETATM 4 O O3B ADP . . . D 3 11.461 80.333 2.057 1 29.74 ? O3B ADP 302 A 1 
HETATM 5 P PA ADP . . . D 3 11.815 83.741 -0.169 1 35.05 ? PA ADP 302 A 1 
HETATM 6 O O1A ADP . . . D 3 11.649 83.3 -1.623 1 37.12 ? O1A ADP 302 A 1 
HETATM 7 O O2A ADP . . . D 3 11.093 84.939 0.382 1 36.57 ? O2A ADP 302 A 1 
HETATM 8 O O3A ADP . . . D 3 11.815 82.553 0.945 1 32.53 ? O3A ADP 302 A 1 
HETATM 9 O O5' ADP . . . D 3 13.383 84.198 -0.111 1 34.23 ? O5' ADP 302 A 1 
HETATM 10 C C5' ADP . . . D 3 13.944 84.801 1.06 1 32.82 ? C5' ADP 302 A 1 
HETATM 11 C C4' ADP . . . D 3 14.839 85.972 0.649 1 33.73 ? C4' ADP 302 A 1 
HETATM 12 O O4' ADP . . . D 3 15.674 85.595 -0.459 1 33.47 ? O4' ADP 302 A 1 
HETATM 13 C C3' ADP . . . D 3 14.041 87.181 0.187 1 35.93 ? C3' ADP 302 A 1 
HETATM 14 O O3' ADP . . . D 3 13.613 88 1.249 1 36.38 ? O3' ADP 302 A 1 
HETATM 15 C C2' ADP . . . D 3 15.055 87.876 -0.678 1 37.98 ? C2' ADP 302 A 1 
HETATM 16 O O2' ADP . . . D 3 15.946 88.648 0.116 1 38.58 ? O2' ADP 302 A 1 
HETATM 17 C C1' ADP . . . D 3 15.811 86.73 -1.317 1 36.47 ? C1' ADP 302 A 1 
HETATM 18 N N9 ADP . . . D 3 15.209 86.435 -2.629 1 38.44 ? N9 ADP 302 A 1 
HETATM 19 C C8 ADP . . . D 3 14.384 85.408 -2.877 1 37.43 ? C8 ADP 302 A 1 
HETATM 20 N N7 ADP . . . D 3 14.027 85.383 -4.155 1 39.63 ? N7 ADP 302 A 1 
HETATM 21 C C5 ADP . . . D 3 14.625 86.403 -4.761 1 42.09 ? C5 ADP 302 A 1 
HETATM 22 C C6 ADP . . . D 3 14.618 86.928 -6.125 1 45.63 ? C6 ADP 302 A 1 
HETATM 23 N N6 ADP . . . D 3 13.901 86.308 -7.078 1 47.38 ? N6 ADP 302 A 1 
HETATM 24 N N1 ADP . . . D 3 15.362 88.03 -6.365 1 48.02 ? N1 ADP 302 A 1 
HETATM 25 C C2 ADP . . . D 3 16.064 88.638 -5.394 1 46.18 ? C2 ADP 302 A 1 
HETATM 26 N N3 ADP . . . D 3 16.103 88.207 -4.121 1 43.64 ? N3 ADP 302 A 1 
HETATM 27 C C4 ADP . . . D 3 15.407 87.115 -3.753 1 40.97 ? C4 ADP 302 A 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           298 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#