data_2HMF
#
_model_server_result.job_id            1zgDM0mKHtVn4Ug154dCVg 
_model_server_result.datetime_utc      '2024-11-13 21:16:19' 
_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          2hmf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":472}' 
#
_entry.id    2HMF 
#
_exptl.entry_id    2HMF 
_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    4 
_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            2HMF 
_cell.length_a            101.741 
_cell.length_b            104.508 
_cell.length_c            192.92 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2HMF 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_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 F N N 
? 3 I N N 
? 3 L N N 
? 3 O 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
metalc ? metalc1 E MG MG . A MG 471 1_555 F O3B ADP . A ADP 472 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? 
metalc ? metalc2 E MG MG . A MG 471 1_555 F O1A ADP . A ADP 472 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? 
metalc ? metalc3 H MG MG . B MG 471 1_555 I O3B ADP . B ADP 472 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? 
metalc ? metalc4 H MG MG . B MG 471 1_555 I O1A ADP . B ADP 472 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? 
metalc ? metalc5 H MG MG . B MG 471 1_555 R O HOH . B HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.563 ? 
metalc ? metalc6 K MG MG . C MG 471 1_555 L O1A ADP . C ADP 472 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? 
metalc ? metalc7 K MG MG . C MG 471 1_555 L O3B ADP . C ADP 472 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? 
metalc ? metalc8 N MG MG . D MG 471 1_555 O O1A ADP . D ADP 472 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? 
metalc ? metalc9 N MG MG . D MG 471 1_555 O O3B ADP . D ADP 472 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
metalc ? metalc10 N MG MG . D MG 471 1_555 T O HOH . D HOH 516 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.553 ? 
#
_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                     2HMF 
_atom_sites.fract_transf_matrix[1][1]    0.009829 
_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]    0.009569 
_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]    0.005183 
_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
E 2 MG A 1 471 1 MG MG . 
F 3 ADP A 1 472 1 ADP ADP . 
G 4 ASP A 1 502 2 ASP LIG . 
H 2 MG B 1 471 2 MG MG . 
I 3 ADP B 1 472 2 ADP ADP . 
J 4 ASP B 1 501 1 ASP LIG . 
K 2 MG C 1 471 3 MG MG . 
L 3 ADP C 1 472 3 ADP ADP . 
M 4 ASP C 1 503 3 ASP LIG . 
N 2 MG D 1 471 4 MG MG . 
O 3 ADP D 1 472 4 ADP ADP . 
P 4 ASP D 1 504 4 ASP LIG . 
Q 5 HOH A 1 503 6 HOH HOH . 
Q 5 HOH A 2 504 12 HOH HOH . 
Q 5 HOH A 3 505 15 HOH HOH . 
Q 5 HOH A 4 506 24 HOH HOH . 
Q 5 HOH A 5 507 32 HOH HOH . 
Q 5 HOH A 6 508 33 HOH HOH . 
Q 5 HOH A 7 509 34 HOH HOH . 
Q 5 HOH A 8 510 35 HOH HOH . 
Q 5 HOH A 9 511 36 HOH HOH . 
Q 5 HOH A 10 512 42 HOH HOH . 
Q 5 HOH A 11 513 47 HOH HOH . 
Q 5 HOH A 12 514 51 HOH HOH . 
Q 5 HOH A 13 515 53 HOH HOH . 
Q 5 HOH A 14 516 57 HOH HOH . 
Q 5 HOH A 15 517 59 HOH HOH . 
Q 5 HOH A 16 518 60 HOH HOH . 
Q 5 HOH A 17 519 61 HOH HOH . 
Q 5 HOH A 18 520 65 HOH HOH . 
Q 5 HOH A 19 521 67 HOH HOH . 
Q 5 HOH A 20 522 68 HOH HOH . 
Q 5 HOH A 21 523 80 HOH HOH . 
Q 5 HOH A 22 524 82 HOH HOH . 
Q 5 HOH A 23 525 92 HOH HOH . 
Q 5 HOH A 24 526 115 HOH HOH . 
Q 5 HOH A 25 527 121 HOH HOH . 
Q 5 HOH A 26 528 124 HOH HOH . 
Q 5 HOH A 27 529 125 HOH HOH . 
Q 5 HOH A 28 530 128 HOH HOH . 
Q 5 HOH A 29 531 144 HOH HOH . 
Q 5 HOH A 30 532 154 HOH HOH . 
Q 5 HOH A 31 533 165 HOH HOH . 
Q 5 HOH A 32 534 169 HOH HOH . 
R 5 HOH B 1 502 9 HOH HOH . 
R 5 HOH B 2 503 10 HOH HOH . 
R 5 HOH B 3 504 13 HOH HOH . 
R 5 HOH B 4 505 20 HOH HOH . 
R 5 HOH B 5 506 23 HOH HOH . 
R 5 HOH B 6 507 26 HOH HOH . 
R 5 HOH B 7 508 28 HOH HOH . 
R 5 HOH B 8 509 30 HOH HOH . 
R 5 HOH B 9 510 43 HOH HOH . 
R 5 HOH B 10 511 45 HOH HOH . 
R 5 HOH B 11 512 56 HOH HOH . 
R 5 HOH B 12 513 70 HOH HOH . 
R 5 HOH B 13 514 76 HOH HOH . 
R 5 HOH B 14 515 87 HOH HOH . 
R 5 HOH B 15 516 89 HOH HOH . 
R 5 HOH B 16 517 96 HOH HOH . 
R 5 HOH B 17 518 97 HOH HOH . 
R 5 HOH B 18 519 105 HOH HOH . 
R 5 HOH B 19 520 107 HOH HOH . 
R 5 HOH B 20 521 108 HOH HOH . 
R 5 HOH B 21 522 113 HOH HOH . 
R 5 HOH B 22 523 118 HOH HOH . 
R 5 HOH B 23 524 120 HOH HOH . 
R 5 HOH B 24 525 122 HOH HOH . 
R 5 HOH B 25 526 130 HOH HOH . 
R 5 HOH B 26 527 132 HOH HOH . 
R 5 HOH B 27 528 136 HOH HOH . 
R 5 HOH B 28 529 143 HOH HOH . 
R 5 HOH B 29 530 155 HOH HOH . 
R 5 HOH B 30 531 159 HOH HOH . 
R 5 HOH B 31 532 161 HOH HOH . 
R 5 HOH B 32 533 178 HOH HOH . 
R 5 HOH B 33 534 182 HOH HOH . 
S 5 HOH C 1 504 3 HOH HOH . 
S 5 HOH C 2 505 16 HOH HOH . 
S 5 HOH C 3 506 19 HOH HOH . 
S 5 HOH C 4 507 27 HOH HOH . 
S 5 HOH C 5 508 29 HOH HOH . 
S 5 HOH C 6 509 38 HOH HOH . 
S 5 HOH C 7 510 64 HOH HOH . 
S 5 HOH C 8 511 74 HOH HOH . 
S 5 HOH C 9 512 94 HOH HOH . 
S 5 HOH C 10 513 99 HOH HOH . 
S 5 HOH C 11 514 103 HOH HOH . 
S 5 HOH C 12 515 104 HOH HOH . 
S 5 HOH C 13 516 110 HOH HOH . 
S 5 HOH C 14 517 117 HOH HOH . 
S 5 HOH C 15 518 123 HOH HOH . 
S 5 HOH C 16 519 129 HOH HOH . 
S 5 HOH C 17 520 147 HOH HOH . 
S 5 HOH C 18 521 150 HOH HOH . 
S 5 HOH C 19 522 164 HOH HOH . 
S 5 HOH C 20 523 180 HOH HOH . 
T 5 HOH D 1 505 2 HOH HOH . 
T 5 HOH D 2 506 4 HOH HOH . 
T 5 HOH D 3 507 5 HOH HOH . 
T 5 HOH D 4 508 14 HOH HOH . 
T 5 HOH D 5 509 18 HOH HOH . 
T 5 HOH D 6 510 22 HOH HOH . 
T 5 HOH D 7 511 31 HOH HOH . 
T 5 HOH D 8 512 37 HOH HOH . 
T 5 HOH D 9 513 40 HOH HOH . 
T 5 HOH D 10 514 46 HOH HOH . 
T 5 HOH D 11 515 52 HOH HOH . 
T 5 HOH D 12 516 71 HOH HOH . 
T 5 HOH D 13 517 72 HOH HOH . 
T 5 HOH D 14 518 73 HOH HOH . 
T 5 HOH D 15 519 78 HOH HOH . 
T 5 HOH D 16 520 79 HOH HOH . 
T 5 HOH D 17 521 81 HOH HOH . 
T 5 HOH D 18 522 83 HOH HOH . 
T 5 HOH D 19 523 86 HOH HOH . 
T 5 HOH D 20 524 88 HOH HOH . 
T 5 HOH D 21 525 95 HOH HOH . 
T 5 HOH D 22 526 100 HOH HOH . 
T 5 HOH D 23 527 102 HOH HOH . 
T 5 HOH D 24 528 109 HOH HOH . 
T 5 HOH D 25 529 111 HOH HOH . 
T 5 HOH D 26 530 126 HOH HOH . 
T 5 HOH D 27 531 131 HOH HOH . 
T 5 HOH D 28 532 134 HOH HOH . 
T 5 HOH D 29 533 135 HOH HOH . 
T 5 HOH D 30 534 141 HOH HOH . 
T 5 HOH D 31 535 142 HOH HOH . 
T 5 HOH D 32 536 151 HOH HOH . 
T 5 HOH D 33 537 152 HOH HOH . 
T 5 HOH D 34 538 157 HOH HOH . 
T 5 HOH D 35 539 158 HOH HOH . 
T 5 HOH D 36 540 163 HOH HOH . 
T 5 HOH D 37 541 167 HOH HOH . 
T 5 HOH D 38 542 175 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 . . . I 3 6.826 -8.729 10.796 1 34.06 ? PB ADP 472 B 1 
HETATM 2 O O1B ADP . . . I 3 7.444 -9.913 10.096 1 33.81 ? O1B ADP 472 B 1 
HETATM 3 O O2B ADP . . . I 3 5.468 -8.423 10.228 1 33.45 ? O2B ADP 472 B 1 
HETATM 4 O O3B ADP . . . I 3 6.913 -8.82 12.315 1 34.64 ? O3B ADP 472 B 1 
HETATM 5 P PA ADP . . . I 3 8.442 -6.388 11.431 1 35.98 ? PA ADP 472 B 1 
HETATM 6 O O1A ADP . . . I 3 7.875 -6.56 12.827 1 36.15 ? O1A ADP 472 B 1 
HETATM 7 O O2A ADP . . . I 3 8.514 -5.018 10.805 1 34.52 ? O2A ADP 472 B 1 
HETATM 8 O O3A ADP . . . I 3 7.726 -7.425 10.389 1 35.66 ? O3A ADP 472 B 1 
HETATM 9 O O5' ADP . . . I 3 9.938 -6.95 11.518 1 36.3 ? O5' ADP 472 B 1 
HETATM 10 C C5' ADP . . . I 3 10.82 -6.988 10.399 1 38.47 ? C5' ADP 472 B 1 
HETATM 11 C C4' ADP . . . I 3 11.662 -5.712 10.36 1 38.36 ? C4' ADP 472 B 1 
HETATM 12 O O4' ADP . . . I 3 12.45 -5.536 11.537 1 38.29 ? O4' ADP 472 B 1 
HETATM 13 C C3' ADP . . . I 3 12.655 -5.696 9.215 1 37.67 ? C3' ADP 472 B 1 
HETATM 14 O O3' ADP . . . I 3 12.011 -5.174 8.045 1 35.98 ? O3' ADP 472 B 1 
HETATM 15 C C2' ADP . . . I 3 13.773 -4.8 9.734 1 37.61 ? C2' ADP 472 B 1 
HETATM 16 O O2' ADP . . . I 3 13.759 -3.54 9.068 1 36.47 ? O2' ADP 472 B 1 
HETATM 17 C C1' ADP . . . I 3 13.455 -4.594 11.21 1 38.7 ? C1' ADP 472 B 1 
HETATM 18 N N9 ADP . . . I 3 14.592 -4.785 12.141 1 39.64 ? N9 ADP 472 B 1 
HETATM 19 C C8 ADP . . . I 3 14.83 -3.98 13.203 1 39.87 ? C8 ADP 472 B 1 
HETATM 20 N N7 ADP . . . I 3 15.938 -4.371 13.894 1 40.01 ? N7 ADP 472 B 1 
HETATM 21 C C5 ADP . . . I 3 16.423 -5.453 13.265 1 39.25 ? C5 ADP 472 B 1 
HETATM 22 C C6 ADP . . . I 3 17.565 -6.359 13.478 1 39.18 ? C6 ADP 472 B 1 
HETATM 23 N N6 ADP . . . I 3 18.404 -6.155 14.523 1 39.28 ? N6 ADP 472 B 1 
HETATM 24 N N1 ADP . . . I 3 17.731 -7.379 12.599 1 39.65 ? N1 ADP 472 B 1 
HETATM 25 C C2 ADP . . . I 3 16.889 -7.575 11.565 1 39.62 ? C2 ADP 472 B 1 
HETATM 26 N N3 ADP . . . I 3 15.826 -6.782 11.317 1 39.48 ? N3 ADP 472 B 1 
HETATM 27 C C4 ADP . . . I 3 15.537 -5.731 12.116 1 39.37 ? C4 ADP 472 B 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    15 
_model_server_stats.query_time_ms           283 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           27 
#