data_8QV2
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_model_server_result.job_id            0RLCEhM8sQinB2sF1U5qBQ 
_model_server_result.datetime_utc      '2024-10-10 01:21:43' 
_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          8qv2 
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_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"ZC","auth_seq_id":501}' 
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_entry.id    8QV2 
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_exptl.entry_id    8QV2 
_exptl.method      'ELECTRON MICROSCOPY' 
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_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          9 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
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_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            8QV2 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
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_symmetry.entry_id                 8QV2 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
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_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    90-meric 
_pdbx_struct_assembly.oligomeric_count      90 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
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_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,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,JB,KB,LB,MB,NB,OB,PB,QB,RB,SB,TB,UB,VB,WB,XB,YB,ZB,AC,BC,CC,DC,EC,FC,GC,HC,IC,JC,KC,LC,MC,NC,OC,PC,QC,RC,SC,TC,UC,VC,WC,XC,YC,ZC,AD,BD,CD,DD,ED,FD,GD 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1 
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_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      9 
_struct_asym.id                             ZC 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
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_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     ? 
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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                     8QV2 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
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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
MC 8 GTP b 1 501 501 GTP GTP . 
NC 8 GTP c 1 501 501 GTP GTP . 
OC 8 GTP d 1 501 501 GTP GTP . 
PC 8 GTP e 1 501 501 GTP GTP . 
QC 8 GTP f 1 501 501 GTP GTP . 
RC 8 GTP g 1 501 501 GTP GTP . 
SC 8 GTP h 1 501 501 GTP GTP . 
TC 8 GTP i 1 501 501 GTP GTP . 
UC 8 GTP j 1 501 501 GTP GTP . 
VC 8 GTP k 1 501 501 GTP GTP . 
WC 8 GTP l 1 501 501 GTP GTP . 
XC 8 GTP m 1 501 501 GTP GTP . 
YC 8 GTP n 1 501 501 GTP GTP . 
ZC 9 GDP a 1 501 501 GDP GDP . 
AD 10 HOH Ue 1 801 803 HOH HOH . 
BD 10 HOH Ui 1 801 803 HOH HOH . 
CD 10 HOH Um 1 801 803 HOH HOH . 
DD 10 HOH Ua 1 801 803 HOH HOH . 
ED 10 HOH Ug 1 801 803 HOH HOH . 
FD 10 HOH Uk 1 801 803 HOH HOH . 
GD 10 HOH Uc 1 801 803 HOH HOH . 
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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 . . . ZC 9 172.012 249.306 320.512 1 999.99 ? PB GDP 501 a 1 
HETATM 2 O O1B GDP . . . ZC 9 171.648 250.495 319.656 1 999.99 ? O1B GDP 501 a 1 
HETATM 3 O O2B GDP . . . ZC 9 171.468 249.502 321.908 1 999.99 ? O2B GDP 501 a 1 
HETATM 4 O O3B GDP . . . ZC 9 173.515 249.176 320.577 1 999.99 ? O3B GDP 501 a 1 
HETATM 5 O O3A GDP . . . ZC 9 171.389 247.967 319.872 1 999.99 ? O3A GDP 501 a 1 
HETATM 6 P PA GDP . . . ZC 9 171.579 247.66 318.303 1 999.99 ? PA GDP 501 a 1 
HETATM 7 O O1A GDP . . . ZC 9 170.589 248.458 317.49 1 999.99 ? O1A GDP 501 a 1 
HETATM 8 O O2A GDP . . . ZC 9 172.992 247.972 317.87 1 999.99 ? O2A GDP 501 a 1 
HETATM 9 O O5' GDP . . . ZC 9 171.283 246.085 318.161 1 999.99 ? O5' GDP 501 a 1 
HETATM 10 C C5' GDP . . . ZC 9 171.709 245.399 316.986 1 999.99 ? C5' GDP 501 a 1 
HETATM 11 C C4' GDP . . . ZC 9 171.201 243.963 316.978 1 999.99 ? C4' GDP 501 a 1 
HETATM 12 O O4' GDP . . . ZC 9 171.755 243.285 315.849 1 999.99 ? O4' GDP 501 a 1 
HETATM 13 C C3' GDP . . . ZC 9 171.633 243.186 318.21 1 999.99 ? C3' GDP 501 a 1 
HETATM 14 O O3' GDP . . . ZC 9 170.513 242.971 319.071 1 999.99 ? O3' GDP 501 a 1 
HETATM 15 C C2' GDP . . . ZC 9 172.162 241.86 317.698 1 999.99 ? C2' GDP 501 a 1 
HETATM 16 O O2' GDP . . . ZC 9 171.331 240.79 318.156 1 999.99 ? O2' GDP 501 a 1 
HETATM 17 C C1' GDP . . . ZC 9 172.118 241.942 316.179 1 999.99 ? C1' GDP 501 a 1 
HETATM 18 N N9 GDP . . . ZC 9 173.463 241.642 315.627 1 999.99 ? N9 GDP 501 a 1 
HETATM 19 C C8 GDP . . . ZC 9 174.574 241.4 316.349 1 999.99 ? C8 GDP 501 a 1 
HETATM 20 N N7 GDP . . . ZC 9 175.643 241.173 315.546 1 999.99 ? N7 GDP 501 a 1 
HETATM 21 C C5 GDP . . . ZC 9 175.222 241.288 314.273 1 999.99 ? C5 GDP 501 a 1 
HETATM 22 C C6 GDP . . . ZC 9 175.838 241.177 312.93 1 999.99 ? C6 GDP 501 a 1 
HETATM 23 O O6 GDP . . . ZC 9 177.049 240.913 312.787 1 999.99 ? O6 GDP 501 a 1 
HETATM 24 N N1 GDP . . . ZC 9 175.057 241.367 311.863 1 999.99 ? N1 GDP 501 a 1 
HETATM 25 C C2 GDP . . . ZC 9 173.749 241.654 311.972 1 999.99 ? C2 GDP 501 a 1 
HETATM 26 N N2 GDP . . . ZC 9 173.046 241.83 310.83 1 999.99 ? N2 GDP 501 a 1 
HETATM 27 N N3 GDP . . . ZC 9 173.114 241.77 313.168 1 999.99 ? N3 GDP 501 a 1 
HETATM 28 C C4 GDP . . . ZC 9 173.787 241.603 314.332 1 999.99 ? C4 GDP 501 a 1 
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_model_server_stats.io_time_ms              363 
_model_server_stats.parse_time_ms           52 
_model_server_stats.create_model_time_ms    311 
_model_server_stats.query_time_ms           268 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           28 
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