data_8CLD
#
_model_server_result.job_id            GjbT49YWAqjux9Tkvkseig 
_model_server_result.datetime_utc      '2024-11-05 10:28:09' 
_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          8cld 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":501}' 
#
_entry.id    8CLD 
#
_exptl.entry_id    8CLD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          8 
_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            8CLD 
_cell.length_a            106.06 
_cell.length_b            159.61 
_cell.length_c            180.61 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8CLD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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,L,M,N,O,P,Q,R,S,T 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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
? 8 J N N 
? 8 O 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 OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? 
metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? 
metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.17 ? 
metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? 
metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? 
metalc ? metalc6 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.557 ? 
metalc ? metalc7 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.712 ? 
metalc ? metalc8 G O2G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.855 ? 
metalc ? metalc9 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.818 ? 
metalc ? metalc10 J O1A GDP . B GDP 501 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.503 ? 
metalc ? metalc11 C OD1 ASP 39 C ASP 39 1_555 N CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? 
metalc ? metalc12 C OD2 ASP 39 C ASP 39 1_555 N CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? 
metalc ? metalc13 C O THR 41 C THR 41 1_555 N CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.588 ? 
metalc ? metalc14 C OG1 THR 41 C THR 41 1_555 N CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? 
metalc ? metalc15 C O GLY 44 C GLY 44 1_555 N CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.99 ? 
metalc ? metalc16 C OE1 GLU 55 C GLU 55 1_555 N CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? 
metalc ? metalc17 C OE2 GLU 55 C GLU 55 1_555 N CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? 
metalc ? metalc18 C OE1 GLU 71 C GLU 71 1_555 M MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.868 ? 
metalc ? metalc19 L O1G GTP . C GTP 501 1_555 M MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? 
metalc ? metalc20 L O1B GTP . C GTP 501 1_555 M MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.943 ? 
#
_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 224 n n 
PB O2B GDP sing 225 n n 
PB O3B GDP sing 226 n n 
PB O3A GDP sing 227 n n 
O2B HOB2 GDP sing 228 n n 
O3B HOB3 GDP sing 229 n n 
O3A PA GDP sing 230 n n 
PA O1A GDP doub 231 n n 
PA O2A GDP sing 232 n n 
PA O5' GDP sing 233 n n 
O2A HOA2 GDP sing 234 n n 
O5' C5' GDP sing 235 n n 
C5' C4' GDP sing 236 n n 
C5' H5' GDP sing 237 n n 
C5' "H5''" GDP sing 238 n n 
C4' O4' GDP sing 239 n n 
C4' C3' GDP sing 240 n n 
C4' H4' GDP sing 241 n n 
O4' C1' GDP sing 242 n n 
C3' O3' GDP sing 243 n n 
C3' C2' GDP sing 244 n n 
C3' H3' GDP sing 245 n n 
O3' HO3' GDP sing 246 n n 
C2' O2' GDP sing 247 n n 
C2' C1' GDP sing 248 n n 
C2' H2' GDP sing 249 n n 
O2' HO2' GDP sing 250 n n 
C1' N9 GDP sing 251 n n 
C1' H1' GDP sing 252 n n 
N9 C8 GDP sing 253 n y 
N9 C4 GDP sing 254 n y 
C8 N7 GDP doub 255 n y 
C8 H8 GDP sing 256 n n 
N7 C5 GDP sing 257 n y 
C5 C6 GDP sing 258 n n 
C5 C4 GDP doub 259 n y 
C6 O6 GDP doub 260 n n 
C6 N1 GDP sing 261 n n 
N1 C2 GDP sing 262 n n 
N1 HN1 GDP sing 263 n n 
C2 N2 GDP sing 264 n n 
C2 N3 GDP doub 265 n n 
N2 HN21 GDP sing 266 n n 
N2 HN22 GDP sing 267 n n 
N3 C4 GDP sing 268 n n 
#
_atom_sites.entry_id                     8CLD 
_atom_sites.fract_transf_matrix[1][1]    0.009429 
_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]    0.006265 
_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]    0.005537 
_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
G 5 GTP A 1 501 501 GTP GTP . 
H 6 MG A 1 502 502 MG MG . 
I 7 CA A 1 503 503 CA CA . 
J 8 GDP B 1 501 504 GDP GDP . 
K 6 MG B 1 502 505 MG MG . 
L 5 GTP C 1 501 506 GTP GTP . 
M 6 MG C 1 502 507 MG MG . 
N 7 CA C 1 503 508 CA CA . 
O 8 GDP D 1 501 509 GDP GTP . 
P 9 BKF D 1 502 510 BKF ANS . 
Q 10 ACP F 1 401 511 ACP ACP . 
R 11 HOH A 1 601 5 HOH HOH . 
S 11 HOH C 1 601 3 HOH HOH . 
T 11 HOH E 1 201 6 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 . . . J 8 18.806 50.702 15.341 1 34.77 ? PB GDP 501 B 1 
HETATM 2 O O1B GDP . . . J 8 17.791 51.128 14.33 1 42.22 ? O1B GDP 501 B 1 
HETATM 3 O O2B GDP . . . J 8 19.513 51.851 15.951 1 44.89 ? O2B GDP 501 B 1 
HETATM 4 O O3B GDP . . . J 8 19.739 49.666 14.811 1 43.35 ? O3B GDP 501 B 1 
HETATM 5 O O3A GDP . . . J 8 17.967 50.034 16.529 1 38.17 ? O3A GDP 501 B 1 
HETATM 6 P PA GDP . . . J 8 16.395 50.05 16.819 1 37.38 ? PA GDP 501 B 1 
HETATM 7 O O1A GDP . . . J 8 15.677 49.595 15.611 1 50.08 ? O1A GDP 501 B 1 
HETATM 8 O O2A GDP . . . J 8 16.002 51.375 17.364 1 31.88 ? O2A GDP 501 B 1 
HETATM 9 O O5' GDP . . . J 8 16.257 48.928 17.948 1 38.18 ? O5' GDP 501 B 1 
HETATM 10 C C5' GDP . . . J 8 14.996 48.232 18.056 1 39.32 ? C5' GDP 501 B 1 
HETATM 11 C C4' GDP . . . J 8 14.519 48.291 19.484 1 33.59 ? C4' GDP 501 B 1 
HETATM 12 O O4' GDP . . . J 8 14.133 49.651 19.793 1 28.91 ? O4' GDP 501 B 1 
HETATM 13 C C3' GDP . . . J 8 13.276 47.462 19.812 1 37.58 ? C3' GDP 501 B 1 
HETATM 14 O O3' GDP . . . J 8 13.219 47.16 21.199 1 30.22 ? O3' GDP 501 B 1 
HETATM 15 C C2' GDP . . . J 8 12.165 48.417 19.379 1 35.64 ? C2' GDP 501 B 1 
HETATM 16 O O2' GDP . . . J 8 10.933 48.129 20.001 1 46.6 ? O2' GDP 501 B 1 
HETATM 17 C C1' GDP . . . J 8 12.729 49.756 19.843 1 31.86 ? C1' GDP 501 B 1 
HETATM 18 N N9 GDP . . . J 8 12.334 50.877 19.002 1 37.73 ? N9 GDP 501 B 1 
HETATM 19 C C8 GDP . . . J 8 12.689 51.087 17.696 1 45.32 ? C8 GDP 501 B 1 
HETATM 20 N N7 GDP . . . J 8 12.186 52.187 17.193 1 40.79 ? N7 GDP 501 B 1 
HETATM 21 C C5 GDP . . . J 8 11.458 52.736 18.238 1 31.76 ? C5 GDP 501 B 1 
HETATM 22 C C6 GDP . . . J 8 10.693 53.924 18.292 1 40.74 ? C6 GDP 501 B 1 
HETATM 23 O O6 GDP . . . J 8 10.503 54.757 17.4 1 53.69 ? O6 GDP 501 B 1 
HETATM 24 N N1 GDP . . . J 8 10.115 54.105 19.545 1 40.15 ? N1 GDP 501 B 1 
HETATM 25 C C2 GDP . . . J 8 10.25 53.254 20.61 1 41.86 ? C2 GDP 501 B 1 
HETATM 26 N N2 GDP . . . J 8 9.617 53.597 21.738 1 40.22 ? N2 GDP 501 B 1 
HETATM 27 N N3 GDP . . . J 8 10.97 52.138 20.567 1 39.88 ? N3 GDP 501 B 1 
HETATM 28 C C4 GDP . . . J 8 11.541 51.94 19.356 1 38.2 ? C4 GDP 501 B 1 
#
_model_server_stats.io_time_ms              53 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           333 
_model_server_stats.encode_time_ms          17 
_model_server_stats.element_count           28 
#