data_3B1W
#
_model_server_result.job_id            dH9R2pSJ-5hVGtvt6llU4g 
_model_server_result.datetime_utc      '2024-12-02 13:37:49' 
_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          3b1w 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":300}' 
#
_entry.id    3B1W 
#
_exptl.entry_id    3B1W 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-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            3B1W 
_cell.length_a            64.6 
_cell.length_b            92.1 
_cell.length_c            206.8 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3B1W 
_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 
PISA monomeric 1 author_and_software_defined_assembly 3 
PISA monomeric 1 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,I 1 1 
B,F,J 2 1 
C,G,K 3 1 
D,H,L 4 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
? 2 E N N 
? 2 F N N 
? 2 G N N 
? 2 H N N 
#
_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                     3B1W 
_atom_sites.fract_transf_matrix[1][1]    0.015483 
_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]    0.010855 
_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]    0.004835 
_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 GDP A 1 300 300 GDP GDP . 
F 2 GDP B 1 300 300 GDP GDP . 
G 2 GDP C 1 300 300 GDP GDP . 
H 2 GDP D 1 300 300 GDP GDP . 
I 3 HOH A 1 271 1 HOH HOH . 
I 3 HOH A 2 272 2 HOH HOH . 
I 3 HOH A 3 273 3 HOH HOH . 
I 3 HOH A 4 274 6 HOH HOH . 
I 3 HOH A 5 275 7 HOH HOH . 
I 3 HOH A 6 276 8 HOH HOH . 
I 3 HOH A 7 277 9 HOH HOH . 
I 3 HOH A 8 278 10 HOH HOH . 
I 3 HOH A 9 279 21 HOH HOH . 
I 3 HOH A 10 280 24 HOH HOH . 
I 3 HOH A 11 281 28 HOH HOH . 
I 3 HOH A 12 282 41 HOH HOH . 
I 3 HOH A 13 283 47 HOH HOH . 
I 3 HOH A 14 284 71 HOH HOH . 
I 3 HOH A 15 285 77 HOH HOH . 
I 3 HOH A 16 286 78 HOH HOH . 
I 3 HOH A 17 287 79 HOH HOH . 
I 3 HOH A 18 288 80 HOH HOH . 
I 3 HOH A 19 289 81 HOH HOH . 
I 3 HOH A 20 290 82 HOH HOH . 
I 3 HOH A 21 291 83 HOH HOH . 
I 3 HOH A 22 292 84 HOH HOH . 
I 3 HOH A 23 293 85 HOH HOH . 
I 3 HOH A 24 294 86 HOH HOH . 
I 3 HOH A 25 295 87 HOH HOH . 
I 3 HOH A 26 296 88 HOH HOH . 
I 3 HOH A 27 297 89 HOH HOH . 
I 3 HOH A 28 298 90 HOH HOH . 
I 3 HOH A 29 299 91 HOH HOH . 
I 3 HOH A 30 301 92 HOH HOH . 
I 3 HOH A 31 302 93 HOH HOH . 
I 3 HOH A 32 303 94 HOH HOH . 
I 3 HOH A 33 304 95 HOH HOH . 
I 3 HOH A 34 305 104 HOH HOH . 
I 3 HOH A 35 306 108 HOH HOH . 
J 3 HOH B 1 271 4 HOH HOH . 
J 3 HOH B 2 272 5 HOH HOH . 
J 3 HOH B 3 273 11 HOH HOH . 
J 3 HOH B 4 274 12 HOH HOH . 
J 3 HOH B 5 275 13 HOH HOH . 
J 3 HOH B 6 276 14 HOH HOH . 
J 3 HOH B 7 277 15 HOH HOH . 
J 3 HOH B 8 278 16 HOH HOH . 
J 3 HOH B 9 279 17 HOH HOH . 
J 3 HOH B 10 280 45 HOH HOH . 
J 3 HOH B 11 281 54 HOH HOH . 
J 3 HOH B 12 282 56 HOH HOH . 
J 3 HOH B 13 283 59 HOH HOH . 
J 3 HOH B 14 284 60 HOH HOH . 
J 3 HOH B 15 285 61 HOH HOH . 
J 3 HOH B 16 286 62 HOH HOH . 
J 3 HOH B 17 287 63 HOH HOH . 
J 3 HOH B 18 288 64 HOH HOH . 
J 3 HOH B 19 289 65 HOH HOH . 
J 3 HOH B 20 290 66 HOH HOH . 
J 3 HOH B 21 291 67 HOH HOH . 
J 3 HOH B 22 292 68 HOH HOH . 
J 3 HOH B 23 293 69 HOH HOH . 
J 3 HOH B 24 294 72 HOH HOH . 
J 3 HOH B 25 295 73 HOH HOH . 
J 3 HOH B 26 296 74 HOH HOH . 
J 3 HOH B 27 297 96 HOH HOH . 
J 3 HOH B 28 298 97 HOH HOH . 
J 3 HOH B 29 299 103 HOH HOH . 
J 3 HOH B 30 301 107 HOH HOH . 
J 3 HOH B 31 302 110 HOH HOH . 
K 3 HOH C 1 271 18 HOH HOH . 
K 3 HOH C 2 272 23 HOH HOH . 
K 3 HOH C 3 273 25 HOH HOH . 
K 3 HOH C 4 274 27 HOH HOH . 
K 3 HOH C 5 275 29 HOH HOH . 
K 3 HOH C 6 276 30 HOH HOH . 
K 3 HOH C 7 277 31 HOH HOH . 
K 3 HOH C 8 278 32 HOH HOH . 
K 3 HOH C 9 279 39 HOH HOH . 
K 3 HOH C 10 280 40 HOH HOH . 
K 3 HOH C 11 281 44 HOH HOH . 
K 3 HOH C 12 282 46 HOH HOH . 
K 3 HOH C 13 283 52 HOH HOH . 
K 3 HOH C 14 284 53 HOH HOH . 
K 3 HOH C 15 285 55 HOH HOH . 
K 3 HOH C 16 286 57 HOH HOH . 
K 3 HOH C 17 287 58 HOH HOH . 
K 3 HOH C 18 288 70 HOH HOH . 
K 3 HOH C 19 289 98 HOH HOH . 
K 3 HOH C 20 290 99 HOH HOH . 
K 3 HOH C 21 291 100 HOH HOH . 
K 3 HOH C 22 292 101 HOH HOH . 
K 3 HOH C 23 293 102 HOH HOH . 
K 3 HOH C 24 294 105 HOH HOH . 
L 3 HOH D 1 271 19 HOH HOH . 
L 3 HOH D 2 272 20 HOH HOH . 
L 3 HOH D 3 273 22 HOH HOH . 
L 3 HOH D 4 274 26 HOH HOH . 
L 3 HOH D 5 275 33 HOH HOH . 
L 3 HOH D 6 276 34 HOH HOH . 
L 3 HOH D 7 277 35 HOH HOH . 
L 3 HOH D 8 278 36 HOH HOH . 
L 3 HOH D 9 279 37 HOH HOH . 
L 3 HOH D 10 280 38 HOH HOH . 
L 3 HOH D 11 281 42 HOH HOH . 
L 3 HOH D 12 282 43 HOH HOH . 
L 3 HOH D 13 283 48 HOH HOH . 
L 3 HOH D 14 284 49 HOH HOH . 
L 3 HOH D 15 285 50 HOH HOH . 
L 3 HOH D 16 286 51 HOH HOH . 
L 3 HOH D 17 287 75 HOH HOH . 
L 3 HOH D 18 288 76 HOH HOH . 
L 3 HOH D 19 289 106 HOH HOH . 
L 3 HOH D 20 290 109 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 2 28.384 -85.707 -11.093 1 36.93 ? PB GDP 300 D 1 
HETATM 2 O O1B GDP . . . H 2 28.688 -84.256 -11.034 1 40.95 ? O1B GDP 300 D 1 
HETATM 3 O O2B GDP . . . H 2 27.644 -86.134 -12.473 1 39.22 ? O2B GDP 300 D 1 
HETATM 4 O O3B GDP . . . H 2 27.387 -86.173 -9.917 1 36.48 ? O3B GDP 300 D 1 
HETATM 5 O O3A GDP . . . H 2 29.708 -86.609 -10.991 1 39.87 ? O3A GDP 300 D 1 
HETATM 6 P PA GDP . . . H 2 29.752 -88.04 -10.17 1 38.61 ? PA GDP 300 D 1 
HETATM 7 O O1A GDP . . . H 2 29.707 -87.858 -8.703 1 42.77 ? O1A GDP 300 D 1 
HETATM 8 O O2A GDP . . . H 2 28.524 -88.928 -10.711 1 39.6 ? O2A GDP 300 D 1 
HETATM 9 O O5' GDP . . . H 2 31.078 -88.744 -10.662 1 39.5 ? O5' GDP 300 D 1 
HETATM 10 C C5' GDP . . . H 2 31.237 -89.097 -12.032 1 42.18 ? C5' GDP 300 D 1 
HETATM 11 C C4' GDP . . . H 2 32.361 -90.158 -12.199 1 44.83 ? C4' GDP 300 D 1 
HETATM 12 O O4' GDP . . . H 2 33.637 -89.603 -11.717 1 44.67 ? O4' GDP 300 D 1 
HETATM 13 C C3' GDP . . . H 2 32.074 -91.432 -11.381 1 45.44 ? C3' GDP 300 D 1 
HETATM 14 O O3' GDP . . . H 2 32.497 -92.565 -12.129 1 46.56 ? O3' GDP 300 D 1 
HETATM 15 C C2' GDP . . . H 2 32.956 -91.26 -10.134 1 46.64 ? C2' GDP 300 D 1 
HETATM 16 O O2' GDP . . . H 2 33.393 -92.516 -9.608 1 49.45 ? O2' GDP 300 D 1 
HETATM 17 C C1' GDP . . . H 2 34.158 -90.461 -10.663 1 44.78 ? C1' GDP 300 D 1 
HETATM 18 N N9 GDP . . . H 2 34.708 -89.523 -9.664 1 44.62 ? N9 GDP 300 D 1 
HETATM 19 C C8 GDP . . . H 2 34.001 -88.728 -8.857 1 45.83 ? C8 GDP 300 D 1 
HETATM 20 N N7 GDP . . . H 2 34.824 -88.017 -8.091 1 44.51 ? N7 GDP 300 D 1 
HETATM 21 C C5 GDP . . . H 2 36.063 -88.351 -8.404 1 45.44 ? C5 GDP 300 D 1 
HETATM 22 C C6 GDP . . . H 2 37.305 -87.932 -7.929 1 47.88 ? C6 GDP 300 D 1 
HETATM 23 O O6 GDP . . . H 2 37.383 -87.076 -7.046 1 48.73 ? O6 GDP 300 D 1 
HETATM 24 N N1 GDP . . . H 2 38.47 -88.492 -8.486 1 47.48 ? N1 GDP 300 D 1 
HETATM 25 C C2 GDP . . . H 2 38.339 -89.459 -9.497 1 46.54 ? C2 GDP 300 D 1 
HETATM 26 N N2 GDP . . . H 2 39.416 -90.01 -10.041 1 47.28 ? N2 GDP 300 D 1 
HETATM 27 N N3 GDP . . . H 2 37.123 -89.837 -9.921 1 46.92 ? N3 GDP 300 D 1 
HETATM 28 C C4 GDP . . . H 2 35.994 -89.311 -9.406 1 45.65 ? C4 GDP 300 D 1 
#
_model_server_stats.io_time_ms              116 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           274 
_model_server_stats.encode_time_ms          14 
_model_server_stats.element_count           28 
#