data_7O83
#
_model_server_result.job_id            -Gn0-1-3J3roq4qnvJ949Q 
_model_server_result.datetime_utc      '2024-11-23 01:32:18' 
_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          7o83 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":202}' 
#
_entry.id    7O83 
#
_exptl.entry_id    7O83 
_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         96.39 
_cell.angle_beta          95.01 
_cell.angle_gamma         103.15 
_cell.entry_id            7O83 
_cell.length_a            33.509 
_cell.length_b            39.227 
_cell.length_c            65.721 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7O83 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 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
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F,J 1 1 
B,G,H,I,K 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 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
covale ? covale1 A SG CYS 13 A CYS 12 1_555 E C V52 . A V52 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.648 ? 
covale ? covale2 B SG CYS 13 B CYS 12 1_555 I C V52 . B V52 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.577 ? 
metalc ? metalc1 A OG SER 18 A SER 17 1_555 C MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? 
metalc ? metalc2 A OE1 GLU 64 A GLU 63 1_555 F CA CA . A CA 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? 
metalc ? metalc3 A OE2 GLU 64 A GLU 63 1_555 F CA CA . A CA 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.814 ? 
metalc ? metalc4 A O GLY 139 A GLY 138 1_555 F CA CA . A CA 204 1_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? 
metalc ? metalc5 C MG MG . A MG 201 1_555 D O3B GDP . A GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? 
metalc ? metalc6 C MG MG . A MG 201 1_555 J O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? 
metalc ? metalc7 C MG MG . A MG 201 1_555 J O HOH . A HOH 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.518 ? 
metalc ? metalc8 C MG MG . A MG 201 1_555 J O HOH . A HOH 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? 
metalc ? metalc9 C MG MG . A MG 201 1_555 J O HOH . A HOH 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? 
metalc ? metalc10 F CA CA . A CA 204 1_555 J O HOH . A HOH 337 1_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.735 ? 
metalc ? metalc11 B OG SER 18 B SER 17 1_555 G MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? 
metalc ? metalc12 G MG MG . B MG 201 1_555 H O1B GDP . B GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? 
metalc ? metalc13 G MG MG . B MG 201 1_555 K O HOH . B HOH 322 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? 
metalc ? metalc14 G MG MG . B MG 201 1_555 K O HOH . B HOH 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? 
metalc ? metalc15 G MG MG . B MG 201 1_555 K O HOH . B HOH 325 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? 
metalc ? metalc16 G MG MG . B MG 201 1_555 K O HOH . B HOH 327 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? 
#
_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                     7O83 
_atom_sites.fract_transf_matrix[1][1]    0.029843 
_atom_sites.fract_transf_matrix[1][2]    0.006972 
_atom_sites.fract_transf_matrix[1][3]    0.003592 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.026179 
_atom_sites.fract_transf_matrix[2][3]    0.003573 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.015416 
_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 MG A 1 201 201 MG MG . 
D 3 GDP A 1 202 206 GDP GDP . 
E 4 V52 A 1 203 1 V52 INH . 
F 5 CA A 1 204 1 CA CA . 
G 2 MG B 1 201 201 MG MG . 
H 3 GDP B 1 202 206 GDP GDP . 
I 4 V52 B 1 203 2 V52 INH . 
J 6 HOH A 1 301 66 HOH HOH . 
J 6 HOH A 2 302 58 HOH HOH . 
J 6 HOH A 3 303 15 HOH HOH . 
J 6 HOH A 4 304 75 HOH HOH . 
J 6 HOH A 5 305 56 HOH HOH . 
J 6 HOH A 6 306 6 HOH HOH . 
J 6 HOH A 7 307 33 HOH HOH . 
J 6 HOH A 8 308 49 HOH HOH . 
J 6 HOH A 9 309 14 HOH HOH . 
J 6 HOH A 10 310 82 HOH HOH . 
J 6 HOH A 11 311 30 HOH HOH . 
J 6 HOH A 12 312 46 HOH HOH . 
J 6 HOH A 13 313 48 HOH HOH . 
J 6 HOH A 14 314 65 HOH HOH . 
J 6 HOH A 15 315 42 HOH HOH . 
J 6 HOH A 16 316 38 HOH HOH . 
J 6 HOH A 17 317 76 HOH HOH . 
J 6 HOH A 18 318 79 HOH HOH . 
J 6 HOH A 19 319 69 HOH HOH . 
J 6 HOH A 20 320 31 HOH HOH . 
J 6 HOH A 21 321 78 HOH HOH . 
J 6 HOH A 22 322 24 HOH HOH . 
J 6 HOH A 23 323 83 HOH HOH . 
J 6 HOH A 24 324 36 HOH HOH . 
J 6 HOH A 25 325 17 HOH HOH . 
J 6 HOH A 26 326 34 HOH HOH . 
J 6 HOH A 27 327 61 HOH HOH . 
J 6 HOH A 28 328 80 HOH HOH . 
J 6 HOH A 29 329 8 HOH HOH . 
J 6 HOH A 30 330 10 HOH HOH . 
J 6 HOH A 31 331 52 HOH HOH . 
J 6 HOH A 32 332 27 HOH HOH . 
J 6 HOH A 33 333 94 HOH HOH . 
J 6 HOH A 34 334 53 HOH HOH . 
J 6 HOH A 35 335 51 HOH HOH . 
J 6 HOH A 36 336 77 HOH HOH . 
J 6 HOH A 37 337 81 HOH HOH . 
K 6 HOH B 1 301 21 HOH HOH . 
K 6 HOH B 2 302 67 HOH HOH . 
K 6 HOH B 3 303 16 HOH HOH . 
K 6 HOH B 4 304 23 HOH HOH . 
K 6 HOH B 5 305 13 HOH HOH . 
K 6 HOH B 6 306 59 HOH HOH . 
K 6 HOH B 7 307 70 HOH HOH . 
K 6 HOH B 8 308 44 HOH HOH . 
K 6 HOH B 9 309 68 HOH HOH . 
K 6 HOH B 10 310 9 HOH HOH . 
K 6 HOH B 11 311 32 HOH HOH . 
K 6 HOH B 12 312 89 HOH HOH . 
K 6 HOH B 13 313 54 HOH HOH . 
K 6 HOH B 14 314 73 HOH HOH . 
K 6 HOH B 15 315 74 HOH HOH . 
K 6 HOH B 16 316 40 HOH HOH . 
K 6 HOH B 17 317 86 HOH HOH . 
K 6 HOH B 18 318 45 HOH HOH . 
K 6 HOH B 19 319 7 HOH HOH . 
K 6 HOH B 20 320 28 HOH HOH . 
K 6 HOH B 21 321 19 HOH HOH . 
K 6 HOH B 22 322 88 HOH HOH . 
K 6 HOH B 23 323 26 HOH HOH . 
K 6 HOH B 24 324 12 HOH HOH . 
K 6 HOH B 25 325 87 HOH HOH . 
K 6 HOH B 26 326 37 HOH HOH . 
K 6 HOH B 27 327 39 HOH HOH . 
K 6 HOH B 28 328 84 HOH HOH . 
K 6 HOH B 29 329 72 HOH HOH . 
K 6 HOH B 30 330 47 HOH HOH . 
K 6 HOH B 31 331 43 HOH HOH . 
K 6 HOH B 32 332 55 HOH HOH . 
K 6 HOH B 33 333 92 HOH HOH . 
K 6 HOH B 34 334 63 HOH HOH . 
K 6 HOH B 35 335 93 HOH HOH . 
K 6 HOH B 36 336 29 HOH HOH . 
K 6 HOH B 37 337 50 HOH HOH . 
K 6 HOH B 38 338 35 HOH HOH . 
K 6 HOH B 39 339 90 HOH HOH . 
K 6 HOH B 40 340 18 HOH HOH . 
K 6 HOH B 41 341 85 HOH HOH . 
K 6 HOH B 42 342 11 HOH HOH . 
K 6 HOH B 43 343 57 HOH HOH . 
K 6 HOH B 44 344 25 HOH HOH . 
K 6 HOH B 45 345 64 HOH HOH . 
K 6 HOH B 46 346 22 HOH HOH . 
K 6 HOH B 47 347 62 HOH HOH . 
K 6 HOH B 48 348 20 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 -11.831 6.5 -32.17 1 10.5 ? PB GDP 202 B 1 
HETATM 2 O O1B GDP . . . H 3 -12.093 6.077 -33.603 1 9.36 ? O1B GDP 202 B 1 
HETATM 3 O O2B GDP . . . H 3 -13.11 6.36 -31.274 1 10.78 ? O2B GDP 202 B 1 
HETATM 4 O O3B GDP . . . H 3 -10.525 6.058 -31.472 1 10.3 ? O3B GDP 202 B 1 
HETATM 5 O O3A GDP . . . H 3 -11.431 8.119 -32.219 1 9.98 ? O3A GDP 202 B 1 
HETATM 6 P PA GDP . . . H 3 -11.831 9.156 -33.45 1 9.58 ? PA GDP 202 B 1 
HETATM 7 O O1A GDP . . . H 3 -10.865 9.063 -34.611 1 9.45 ? O1A GDP 202 B 1 
HETATM 8 O O2A GDP . . . H 3 -13.319 8.938 -33.653 1 8.96 ? O2A GDP 202 B 1 
HETATM 9 O O5' GDP . . . H 3 -11.502 10.587 -32.754 1 10.39 ? O5' GDP 202 B 1 
HETATM 10 C C5' GDP . . . H 3 -12.159 11.12 -31.564 1 10.76 ? C5' GDP 202 B 1 
HETATM 11 C C4' GDP . . . H 3 -12 12.644 -31.525 1 11.23 ? C4' GDP 202 B 1 
HETATM 12 O O4' GDP . . . H 3 -10.619 13.061 -31.37 1 11.51 ? O4' GDP 202 B 1 
HETATM 13 C C3' GDP . . . H 3 -12.478 13.221 -32.855 1 11.66 ? C3' GDP 202 B 1 
HETATM 14 O O3' GDP . . . H 3 -13.28 14.37 -32.661 1 13.09 ? O3' GDP 202 B 1 
HETATM 15 C C2' GDP . . . H 3 -11.2 13.475 -33.661 1 11.62 ? C2' GDP 202 B 1 
HETATM 16 O O2' GDP . . . H 3 -11.273 14.478 -34.64 1 11.5 ? O2' GDP 202 B 1 
HETATM 17 C C1' GDP . . . H 3 -10.173 13.765 -32.606 1 11.52 ? C1' GDP 202 B 1 
HETATM 18 N N9 GDP . . . H 3 -8.786 13.362 -32.976 1 11.28 ? N9 GDP 202 B 1 
HETATM 19 C C8 GDP . . . H 3 -8.299 12.166 -33.473 1 11.46 ? C8 GDP 202 B 1 
HETATM 20 N N7 GDP . . . H 3 -6.957 12.184 -33.598 1 10.56 ? N7 GDP 202 B 1 
HETATM 21 C C5 GDP . . . H 3 -6.574 13.398 -33.168 1 10.35 ? C5 GDP 202 B 1 
HETATM 22 C C6 GDP . . . H 3 -5.307 14.117 -33.01 1 10.37 ? C6 GDP 202 B 1 
HETATM 23 O O6 GDP . . . H 3 -4.231 13.574 -33.308 1 9.86 ? O6 GDP 202 B 1 
HETATM 24 N N1 GDP . . . H 3 -5.37 15.379 -32.528 1 10.67 ? N1 GDP 202 B 1 
HETATM 25 C C2 GDP . . . H 3 -6.54 15.998 -32.177 1 10.68 ? C2 GDP 202 B 1 
HETATM 26 N N2 GDP . . . H 3 -6.589 17.251 -31.687 1 10.91 ? N2 GDP 202 B 1 
HETATM 27 N N3 GDP . . . H 3 -7.729 15.409 -32.304 1 10.83 ? N3 GDP 202 B 1 
HETATM 28 C C4 GDP . . . H 3 -7.775 14.146 -32.775 1 10.83 ? C4 GDP 202 B 1 
#
_model_server_stats.io_time_ms              48 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    28 
_model_server_stats.query_time_ms           298 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           28 
#