data_6VS4
#
_model_server_result.job_id            YKQtb-kXlYX6ijOu-DOxDw 
_model_server_result.datetime_utc      '2025-03-12 20:02:27' 
_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          6vs4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":302}' 
#
_entry.id    6VS4 
#
_exptl.entry_id    6VS4 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            6VS4 
_cell.length_a            65.19 
_cell.length_b            65.19 
_cell.length_c            307.71 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6VS4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    'P 4nw 2abw' 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 7_556 y,x,-z+1 0 1 0 1 0 0 0 0 -1 0 0 307.71 
#
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 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 53 A THR 49 1_555 E MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? 
metalc ? metalc2 D O2B GDP . A GDP 302 1_555 E MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? 
metalc ? metalc3 E MG MG . A MG 303 1_555 J O HOH . A HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? 
metalc ? metalc4 E MG MG . A MG 303 1_555 J O HOH . A HOH 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? 
metalc ? metalc5 B OG1 THR 53 B THR 49 1_555 I MG MG . B MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? 
metalc ? metalc6 H O2B GDP . B GDP 303 1_555 I MG MG . B MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? 
metalc ? metalc7 I MG MG . B MG 304 1_555 K O HOH . B HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? 
metalc ? metalc8 I MG MG . B MG 304 1_555 K O HOH . B HOH 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? 
metalc ? metalc9 I MG MG . B MG 304 1_555 K O HOH . B HOH 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? 
metalc ? metalc10 I MG MG . B MG 304 1_555 K O HOH . B HOH 421 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? 
#
_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                     6VS4 
_atom_sites.fract_transf_matrix[1][1]    0.01534 
_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]    0.01534 
_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]    0.00325 
_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 PEG A 1 301 400 PEG PEG . 
D 3 GDP A 1 302 300 GDP GDP . 
E 4 MG A 1 303 301 MG MG . 
F 2 PEG B 1 301 400 PEG PEG . 
G 2 PEG B 1 302 401 PEG PEG . 
H 3 GDP B 1 303 300 GDP GDP . 
I 4 MG B 1 304 301 MG MG . 
J 5 HOH A 1 401 40 HOH HOH . 
J 5 HOH A 2 402 38 HOH HOH . 
J 5 HOH A 3 403 48 HOH HOH . 
J 5 HOH A 4 404 91 HOH HOH . 
J 5 HOH A 5 405 32 HOH HOH . 
J 5 HOH A 6 406 67 HOH HOH . 
J 5 HOH A 7 407 24 HOH HOH . 
J 5 HOH A 8 408 84 HOH HOH . 
J 5 HOH A 9 409 10 HOH HOH . 
J 5 HOH A 10 410 92 HOH HOH . 
J 5 HOH A 11 411 42 HOH HOH . 
J 5 HOH A 12 412 69 HOH HOH . 
J 5 HOH A 13 413 72 HOH HOH . 
J 5 HOH A 14 414 116 HOH HOH . 
J 5 HOH A 15 415 6 HOH HOH . 
J 5 HOH A 16 416 117 HOH HOH . 
J 5 HOH A 17 417 9 HOH HOH . 
J 5 HOH A 18 418 41 HOH HOH . 
J 5 HOH A 19 419 77 HOH HOH . 
J 5 HOH A 20 420 157 HOH HOH . 
J 5 HOH A 21 421 83 HOH HOH . 
J 5 HOH A 22 422 66 HOH HOH . 
J 5 HOH A 23 423 76 HOH HOH . 
J 5 HOH A 24 424 85 HOH HOH . 
J 5 HOH A 25 425 62 HOH HOH . 
J 5 HOH A 26 426 20 HOH HOH . 
J 5 HOH A 27 427 34 HOH HOH . 
J 5 HOH A 28 428 31 HOH HOH . 
J 5 HOH A 29 429 156 HOH HOH . 
J 5 HOH A 30 430 37 HOH HOH . 
J 5 HOH A 31 431 4 HOH HOH . 
J 5 HOH A 32 432 82 HOH HOH . 
J 5 HOH A 33 433 27 HOH HOH . 
J 5 HOH A 34 434 74 HOH HOH . 
J 5 HOH A 35 435 86 HOH HOH . 
J 5 HOH A 36 436 21 HOH HOH . 
J 5 HOH A 37 437 80 HOH HOH . 
J 5 HOH A 38 438 61 HOH HOH . 
J 5 HOH A 39 439 113 HOH HOH . 
J 5 HOH A 40 440 13 HOH HOH . 
J 5 HOH A 41 441 118 HOH HOH . 
K 5 HOH B 1 401 132 HOH HOH . 
K 5 HOH B 2 402 52 HOH HOH . 
K 5 HOH B 3 403 99 HOH HOH . 
K 5 HOH B 4 404 55 HOH HOH . 
K 5 HOH B 5 405 17 HOH HOH . 
K 5 HOH B 6 406 12 HOH HOH . 
K 5 HOH B 7 407 103 HOH HOH . 
K 5 HOH B 8 408 28 HOH HOH . 
K 5 HOH B 9 409 96 HOH HOH . 
K 5 HOH B 10 410 11 HOH HOH . 
K 5 HOH B 11 411 5 HOH HOH . 
K 5 HOH B 12 412 90 HOH HOH . 
K 5 HOH B 13 413 142 HOH HOH . 
K 5 HOH B 14 414 126 HOH HOH . 
K 5 HOH B 15 415 3 HOH HOH . 
K 5 HOH B 16 416 8 HOH HOH . 
K 5 HOH B 17 417 108 HOH HOH . 
K 5 HOH B 18 418 88 HOH HOH . 
K 5 HOH B 19 419 145 HOH HOH . 
K 5 HOH B 20 420 100 HOH HOH . 
K 5 HOH B 21 421 89 HOH HOH . 
K 5 HOH B 22 422 30 HOH HOH . 
K 5 HOH B 23 423 130 HOH HOH . 
K 5 HOH B 24 424 97 HOH HOH . 
K 5 HOH B 25 425 18 HOH HOH . 
K 5 HOH B 26 426 95 HOH HOH . 
K 5 HOH B 27 427 7 HOH HOH . 
K 5 HOH B 28 428 110 HOH HOH . 
K 5 HOH B 29 429 29 HOH HOH . 
K 5 HOH B 30 430 60 HOH HOH . 
K 5 HOH B 31 431 107 HOH HOH . 
K 5 HOH B 32 432 111 HOH HOH . 
K 5 HOH B 33 433 16 HOH HOH . 
K 5 HOH B 34 434 15 HOH HOH . 
K 5 HOH B 35 435 139 HOH HOH . 
K 5 HOH B 36 436 51 HOH HOH . 
K 5 HOH B 37 437 87 HOH HOH . 
K 5 HOH B 38 438 102 HOH HOH . 
K 5 HOH B 39 439 26 HOH HOH . 
K 5 HOH B 40 440 50 HOH HOH . 
K 5 HOH B 41 441 58 HOH HOH . 
K 5 HOH B 42 442 124 HOH HOH . 
K 5 HOH B 43 443 93 HOH HOH . 
K 5 HOH B 44 444 101 HOH HOH . 
K 5 HOH B 45 445 36 HOH HOH . 
K 5 HOH B 46 446 144 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 . . . D 3 13.279 32.436 125.04 1 59.19 ? PB GDP 302 A 1 
HETATM 2 O O1B GDP . . . D 3 12.723 31.77 123.768 1 64.44 ? O1B GDP 302 A 1 
HETATM 3 O O2B GDP . . . D 3 12.362 32.277 126.216 1 66.03 ? O2B GDP 302 A 1 
HETATM 4 O O3B GDP . . . D 3 13.623 33.889 124.704 1 48.78 ? O3B GDP 302 A 1 
HETATM 5 O O3A GDP . . . D 3 14.678 31.748 125.353 1 41.84 ? O3A GDP 302 A 1 
HETATM 6 P PA GDP . . . D 3 15.275 30.987 126.61 1 57.44 ? PA GDP 302 A 1 
HETATM 7 O O1A GDP . . . D 3 14.607 29.622 126.658 1 63.76 ? O1A GDP 302 A 1 
HETATM 8 O O2A GDP . . . D 3 15.184 31.807 127.835 1 65.19 ? O2A GDP 302 A 1 
HETATM 9 O O5' GDP . . . D 3 16.799 30.721 126.217 1 65.96 ? O5' GDP 302 A 1 
HETATM 10 C C5' GDP . . . D 3 17.218 29.884 125.119 1 66.58 ? C5' GDP 302 A 1 
HETATM 11 C C4' GDP . . . D 3 18.589 29.328 125.411 1 58.76 ? C4' GDP 302 A 1 
HETATM 12 O O4' GDP . . . D 3 19.543 30.411 125.495 1 54.37 ? O4' GDP 302 A 1 
HETATM 13 C C3' GDP . . . D 3 18.713 28.527 126.713 1 62.61 ? C3' GDP 302 A 1 
HETATM 14 O O3' GDP . . . D 3 19.386 27.29 126.506 1 66.79 ? O3' GDP 302 A 1 
HETATM 15 C C2' GDP . . . D 3 19.517 29.459 127.626 1 59.69 ? C2' GDP 302 A 1 
HETATM 16 O O2' GDP . . . D 3 20.321 28.72 128.535 1 63 ? O2' GDP 302 A 1 
HETATM 17 C C1' GDP . . . D 3 20.387 30.179 126.603 1 58.11 ? C1' GDP 302 A 1 
HETATM 18 N N9 GDP . . . D 3 20.924 31.469 127.063 1 60.87 ? N9 GDP 302 A 1 
HETATM 19 C C8 GDP . . . D 3 20.241 32.524 127.612 1 57.81 ? C8 GDP 302 A 1 
HETATM 20 N N7 GDP . . . D 3 21.018 33.532 127.933 1 51.54 ? N7 GDP 302 A 1 
HETATM 21 C C5 GDP . . . D 3 22.291 33.11 127.58 1 61.03 ? C5 GDP 302 A 1 
HETATM 22 C C6 GDP . . . D 3 23.573 33.744 127.719 1 58.41 ? C6 GDP 302 A 1 
HETATM 23 O O6 GDP . . . D 3 23.806 34.868 128.153 1 54.84 ? O6 GDP 302 A 1 
HETATM 24 N N1 GDP . . . D 3 24.601 32.942 127.266 1 57.91 ? N1 GDP 302 A 1 
HETATM 25 C C2 GDP . . . D 3 24.447 31.697 126.717 1 59.26 ? C2 GDP 302 A 1 
HETATM 26 N N2 GDP . . . D 3 25.555 31.069 126.32 1 55.86 ? N2 GDP 302 A 1 
HETATM 27 N N3 GDP . . . D 3 23.267 31.101 126.573 1 63.31 ? N3 GDP 302 A 1 
HETATM 28 C C4 GDP . . . D 3 22.244 31.847 127.034 1 64.07 ? C4 GDP 302 A 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           309 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#