data_7MO3
#
_model_server_result.job_id            byFEc_XJV4Kd6KQfPUctHg 
_model_server_result.datetime_utc      '2024-10-18 15:25:21' 
_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          7mo3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":301}' 
#
_entry.id    7MO3 
#
_exptl.entry_id    7MO3 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-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          105.12 
_cell.angle_gamma         90 
_cell.entry_id            7MO3 
_cell.length_a            68.97 
_cell.length_b            62.55 
_cell.length_c            70.65 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7MO3 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
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 dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 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,B,E,F,G,K,L 1 1 
C,D,H,I,J,M 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 E N N 
? 3 H 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 A OG1 THR 25 A THR 24 1_555 F MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? 
metalc ? metalc2 E O2B GDP . A GDP 301 1_555 F MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
metalc ? metalc3 F MG MG . A MG 302 1_555 K O HOH . A HOH 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? 
metalc ? metalc4 F MG MG . A MG 302 1_555 K O HOH . A HOH 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? 
metalc ? metalc5 F MG MG . A MG 302 1_555 K O HOH . A HOH 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? 
metalc ? metalc6 F MG MG . A MG 302 1_555 K O HOH . A HOH 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
metalc ? metalc7 B SG CYS 20 B CYS 795 1_555 G ZN ZN . B ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? 
metalc ? metalc8 B SG CYS 23 B CYS 798 1_555 G ZN ZN . B ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? 
metalc ? metalc9 B SG CYS 34 B CYS 809 1_555 G ZN ZN . B ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? 
metalc ? metalc10 B SG CYS 37 B CYS 812 1_555 G ZN ZN . B ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? 
metalc ? metalc11 C OG1 THR 25 C THR 24 1_555 I MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? 
metalc ? metalc12 H O1B GDP . C GDP 301 1_555 I MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
metalc ? metalc13 I MG MG . C MG 302 1_555 M O HOH . C HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
metalc ? metalc14 I MG MG . C MG 302 1_555 M O HOH . C HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? 
metalc ? metalc15 I MG MG . C MG 302 1_555 M O HOH . C HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? 
metalc ? metalc16 I MG MG . C MG 302 1_555 M O HOH . C HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? 
metalc ? metalc17 D SG CYS 20 D CYS 795 1_555 J ZN ZN . D ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? 
metalc ? metalc18 D SG CYS 23 D CYS 798 1_555 J ZN ZN . D ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? 
metalc ? metalc19 D SG CYS 34 D CYS 809 1_555 J ZN ZN . D ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? 
metalc ? metalc20 D SG CYS 37 D CYS 812 1_555 J ZN ZN . D ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? 
#
_chem_comp.formula           'C10 H15 N5 O11 P2' 
_chem_comp.formula_weight    443.201 
_chem_comp.id                GDP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "GUANOSINE-5'-DIPHOSPHATE" 
_chem_comp.type              'rna linking' 
_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 GDP doub 83 n n 
PB O2B GDP sing 84 n n 
PB O3B GDP sing 85 n n 
PB O3A GDP sing 86 n n 
O2B HOB2 GDP sing 87 n n 
O3B HOB3 GDP sing 88 n n 
O3A PA GDP sing 89 n n 
PA O1A GDP doub 90 n n 
PA O2A GDP sing 91 n n 
PA O5' GDP sing 92 n n 
O2A HOA2 GDP sing 93 n n 
O5' C5' GDP sing 94 n n 
C5' C4' GDP sing 95 n n 
C5' H5' GDP sing 96 n n 
C5' "H5''" GDP sing 97 n n 
C4' O4' GDP sing 98 n n 
C4' C3' GDP sing 99 n n 
C4' H4' GDP sing 100 n n 
O4' C1' GDP sing 101 n n 
C3' O3' GDP sing 102 n n 
C3' C2' GDP sing 103 n n 
C3' H3' GDP sing 104 n n 
O3' HO3' GDP sing 105 n n 
C2' O2' GDP sing 106 n n 
C2' C1' GDP sing 107 n n 
C2' H2' GDP sing 108 n n 
O2' HO2' GDP sing 109 n n 
C1' N9 GDP sing 110 n n 
C1' H1' GDP sing 111 n n 
N9 C8 GDP sing 112 n y 
N9 C4 GDP sing 113 n y 
C8 N7 GDP doub 114 n y 
C8 H8 GDP sing 115 n n 
N7 C5 GDP sing 116 n y 
C5 C6 GDP sing 117 n n 
C5 C4 GDP doub 118 n y 
C6 O6 GDP doub 119 n n 
C6 N1 GDP sing 120 n n 
N1 C2 GDP sing 121 n n 
N1 HN1 GDP sing 122 n n 
C2 N2 GDP sing 123 n n 
C2 N3 GDP doub 124 n n 
N2 HN21 GDP sing 125 n n 
N2 HN22 GDP sing 126 n n 
N3 C4 GDP sing 127 n n 
#
_atom_sites.entry_id                     7MO3 
_atom_sites.fract_transf_matrix[1][1]    0.014499 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.003918 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.015987 
_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]    0.014662 
_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 3 GDP A 1 301 301 GDP GDP . 
F 4 MG A 1 302 401 MG MG . 
G 5 ZN B 1 901 901 ZN ZN . 
H 3 GDP C 1 301 301 GDP GDP . 
I 4 MG C 1 302 401 MG MG . 
J 5 ZN D 1 901 901 ZN ZN . 
K 6 HOH A 1 401 574 HOH HOH . 
K 6 HOH A 2 402 544 HOH HOH . 
K 6 HOH A 3 403 562 HOH HOH . 
K 6 HOH A 4 404 518 HOH HOH . 
K 6 HOH A 5 405 527 HOH HOH . 
K 6 HOH A 6 406 517 HOH HOH . 
K 6 HOH A 7 407 546 HOH HOH . 
K 6 HOH A 8 408 523 HOH HOH . 
K 6 HOH A 9 409 501 HOH HOH . 
K 6 HOH A 10 410 547 HOH HOH . 
K 6 HOH A 11 411 532 HOH HOH . 
K 6 HOH A 12 412 502 HOH HOH . 
K 6 HOH A 13 413 503 HOH HOH . 
K 6 HOH A 14 414 508 HOH HOH . 
K 6 HOH A 15 415 533 HOH HOH . 
K 6 HOH A 16 416 519 HOH HOH . 
K 6 HOH A 17 417 515 HOH HOH . 
K 6 HOH A 18 418 536 HOH HOH . 
K 6 HOH A 19 419 535 HOH HOH . 
K 6 HOH A 20 420 528 HOH HOH . 
K 6 HOH A 21 421 569 HOH HOH . 
K 6 HOH A 22 422 565 HOH HOH . 
K 6 HOH A 23 423 504 HOH HOH . 
K 6 HOH A 24 424 526 HOH HOH . 
K 6 HOH A 25 425 509 HOH HOH . 
K 6 HOH A 26 426 505 HOH HOH . 
K 6 HOH A 27 427 556 HOH HOH . 
K 6 HOH A 28 428 507 HOH HOH . 
K 6 HOH A 29 429 570 HOH HOH . 
K 6 HOH A 30 430 554 HOH HOH . 
K 6 HOH A 31 431 548 HOH HOH . 
K 6 HOH A 32 432 511 HOH HOH . 
K 6 HOH A 33 433 520 HOH HOH . 
K 6 HOH A 34 434 530 HOH HOH . 
K 6 HOH A 35 435 510 HOH HOH . 
K 6 HOH A 36 436 555 HOH HOH . 
K 6 HOH A 37 437 506 HOH HOH . 
K 6 HOH A 38 438 552 HOH HOH . 
K 6 HOH A 39 439 522 HOH HOH . 
K 6 HOH A 40 440 549 HOH HOH . 
K 6 HOH A 41 441 545 HOH HOH . 
K 6 HOH A 42 442 575 HOH HOH . 
K 6 HOH A 43 443 534 HOH HOH . 
K 6 HOH A 44 444 553 HOH HOH . 
K 6 HOH A 45 445 566 HOH HOH . 
K 6 HOH A 46 446 551 HOH HOH . 
K 6 HOH A 47 447 579 HOH HOH . 
K 6 HOH A 48 448 525 HOH HOH . 
K 6 HOH A 49 449 521 HOH HOH . 
K 6 HOH A 50 450 564 HOH HOH . 
K 6 HOH A 51 451 578 HOH HOH . 
K 6 HOH A 52 452 550 HOH HOH . 
L 6 HOH B 1 1001 529 HOH HOH . 
M 6 HOH C 1 401 573 HOH HOH . 
M 6 HOH C 2 402 502 HOH HOH . 
M 6 HOH C 3 403 504 HOH HOH . 
M 6 HOH C 4 404 540 HOH HOH . 
M 6 HOH C 5 405 501 HOH HOH . 
M 6 HOH C 6 406 503 HOH HOH . 
M 6 HOH C 7 407 567 HOH HOH . 
M 6 HOH C 8 408 563 HOH HOH . 
M 6 HOH C 9 409 557 HOH HOH . 
M 6 HOH C 10 410 572 HOH HOH . 
M 6 HOH C 11 411 571 HOH HOH . 
M 6 HOH C 12 412 538 HOH HOH . 
M 6 HOH C 13 413 560 HOH HOH . 
M 6 HOH C 14 414 539 HOH HOH . 
M 6 HOH C 15 415 531 HOH HOH . 
M 6 HOH C 16 416 513 HOH HOH . 
M 6 HOH C 17 417 543 HOH HOH . 
M 6 HOH C 18 418 541 HOH HOH . 
M 6 HOH C 19 419 537 HOH HOH . 
M 6 HOH C 20 420 524 HOH HOH . 
M 6 HOH C 21 421 514 HOH HOH . 
M 6 HOH C 22 422 512 HOH HOH . 
M 6 HOH C 23 423 542 HOH HOH . 
M 6 HOH C 24 424 558 HOH HOH . 
M 6 HOH C 25 425 568 HOH HOH . 
M 6 HOH C 26 426 516 HOH HOH . 
M 6 HOH C 27 427 561 HOH HOH . 
M 6 HOH C 28 428 577 HOH HOH . 
M 6 HOH C 29 429 576 HOH HOH . 
M 6 HOH C 30 430 559 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 GDP . . . H 3 28.573 6.479 2.851 1 70.24 ? PB GDP 301 C 1 
HETATM 2 O O1B GDP . . . H 3 28.48 6.711 1.356 1 69.63 ? O1B GDP 301 C 1 
HETATM 3 O O2B GDP . . . H 3 29.729 5.541 3.114 1 79.23 ? O2B GDP 301 C 1 
HETATM 4 O O3B GDP . . . H 3 28.785 7.789 3.571 1 72.64 ? O3B GDP 301 C 1 
HETATM 5 O O3A GDP . . . H 3 27.194 5.794 3.399 1 63.6 ? O3A GDP 301 C 1 
HETATM 6 P PA GDP . . . H 3 26.255 4.817 2.467 1 68.78 ? PA GDP 301 C 1 
HETATM 7 O O1A GDP . . . H 3 25.474 5.664 1.485 1 70.95 ? O1A GDP 301 C 1 
HETATM 8 O O2A GDP . . . H 3 27.129 3.821 1.711 1 71.05 ? O2A GDP 301 C 1 
HETATM 9 O O5' GDP . . . H 3 25.191 4.006 3.473 1 66.19 ? O5' GDP 301 C 1 
HETATM 10 C C5' GDP . . . H 3 25.768 3.236 4.503 1 72.67 ? C5' GDP 301 C 1 
HETATM 11 C C4' GDP . . . H 3 24.64 2.343 5.184 1 70.73 ? C4' GDP 301 C 1 
HETATM 12 O O4' GDP . . . H 3 23.688 3.337 5.93 1 65.52 ? O4' GDP 301 C 1 
HETATM 13 C C3' GDP . . . H 3 23.968 1.751 4.317 1 71.13 ? C3' GDP 301 C 1 
HETATM 14 O O3' GDP . . . H 3 23.714 0.351 4.771 1 75.16 ? O3' GDP 301 C 1 
HETATM 15 C C2' GDP . . . H 3 22.513 2.558 4.18 1 70.84 ? C2' GDP 301 C 1 
HETATM 16 O O2' GDP . . . H 3 21.448 1.62 3.841 1 70.77 ? O2' GDP 301 C 1 
HETATM 17 C C1' GDP . . . H 3 22.295 2.995 5.351 1 72.23 ? C1' GDP 301 C 1 
HETATM 18 N N9 GDP . . . H 3 21.41 4.207 5.433 1 72.74 ? N9 GDP 301 C 1 
HETATM 19 C C8 GDP . . . H 3 22.007 5.219 4.753 1 70.7 ? C8 GDP 301 C 1 
HETATM 20 N N7 GDP . . . H 3 21.201 6.292 4.818 1 70.98 ? N7 GDP 301 C 1 
HETATM 21 C C5 GDP . . . H 3 20.135 5.957 5.546 1 73.05 ? C5 GDP 301 C 1 
HETATM 22 C C6 GDP . . . H 3 18.885 6.738 5.981 1 73.18 ? C6 GDP 301 C 1 
HETATM 23 O O6 GDP . . . H 3 18.749 7.881 5.651 1 73.12 ? O6 GDP 301 C 1 
HETATM 24 N N1 GDP . . . H 3 17.887 6.097 6.782 1 76.64 ? N1 GDP 301 C 1 
HETATM 25 C C2 GDP . . . H 3 18.059 4.724 7.175 1 76.38 ? C2 GDP 301 C 1 
HETATM 26 N N2 GDP . . . H 3 17.051 4.043 7.994 1 78.28 ? N2 GDP 301 C 1 
HETATM 27 N N3 GDP . . . H 3 19.256 3.984 6.755 1 72.67 ? N3 GDP 301 C 1 
HETATM 28 C C4 GDP . . . H 3 20.279 4.658 5.929 1 74.62 ? C4 GDP 301 C 1 
HETATM 29 H H5' GDP . . . H 3 26.161 3.824 5.167 1 87.22 ? H5' GDP 301 C 1 
HETATM 30 H "H5''" GDP . . . H 3 26.456 2.662 4.132 1 87.22 ? "H5''" GDP 301 C 1 
HETATM 31 H H4' GDP . . . H 3 24.992 1.67 5.787 1 84.9 ? H4' GDP 301 C 1 
HETATM 32 H H3' GDP . . . H 3 24.434 1.782 3.467 1 85.38 ? H3' GDP 301 C 1 
HETATM 33 H HO3' GDP . . . H 3 23.906 -0.199 4.151 1 90.21 ? HO3' GDP 301 C 1 
HETATM 34 H H2' GDP . . . H 3 22.576 3.269 3.523 1 85.02 ? H2' GDP 301 C 1 
HETATM 35 H HO2' GDP . . . H 3 21.215 1.738 3.031 1 84.95 ? HO2' GDP 301 C 1 
HETATM 36 H H1' GDP . . . H 3 21.859 2.275 5.832 1 86.69 ? H1' GDP 301 C 1 
HETATM 37 H H8 GDP . . . H 3 22.828 5.177 4.319 1 84.86 ? H8 GDP 301 C 1 
HETATM 38 H HN1 GDP . . . H 3 17.186 6.532 7.027 1 91.99 ? HN1 GDP 301 C 1 
HETATM 39 H HN21 GDP . . . H 3 17.172 3.221 8.219 1 93.96 ? HN21 GDP 301 C 1 
HETATM 40 H HN22 GDP . . . H 3 16.346 4.464 8.246 1 93.96 ? HN22 GDP 301 C 1 
#
_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           313 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           40 
#