data_3IR6
#
_model_server_result.job_id            GNKFVAQHSFnvXx8ryhJRVg 
_model_server_result.datetime_utc      '2024-11-24 04:40:19' 
_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          3ir6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1247}' 
#
_entry.id    3IR6 
#
_exptl.entry_id    3IR6 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          4 
_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            3IR6 
_cell.length_a            154.142 
_cell.length_b            239.825 
_cell.length_c            139.873 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3IR6 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 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 trimeric 3 author_and_software_defined_assembly 1 
PISA hexameric 6 software_defined_assembly 2 
PISA hexameric 6 software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F,G,H,I,J,K,L,M,N,O 1 1 
A,B,C,D,E,F,G,H,I,J,K,L,M,N,O 2 1,2 
A,B,C,D,E,F,G,H,I,J,K,L,M,N,O 3 1,3 
#
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' 3_354 -x-2,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 -308.284 0 -69.9365 
3 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 D N N 
? 4 E 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 C C FME 1 C FME 1 1_555 C N GLN 2 C GLN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.353 ? 
metalc ? metalc1 B SG CYS 16 B CYS 16 1_555 G FE4 SF4 . B SF4 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? 
metalc ? metalc2 B SG CYS 19 B CYS 19 1_555 G FE3 SF4 . B SF4 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? 
metalc ? metalc3 B SG CYS 22 B CYS 22 1_555 G FE2 SF4 . B SF4 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? 
metalc ? metalc4 B SG CYS 26 B CYS 26 1_555 H FE4 SF4 . B SF4 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? 
metalc ? metalc5 B SG CYS 184 B CYS 184 1_555 I FE1 SF4 . B SF4 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? 
metalc ? metalc6 B SG CYS 187 B CYS 187 1_555 I FE2 SF4 . B SF4 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? 
metalc ? metalc7 B SG CYS 192 B CYS 192 1_555 I FE3 SF4 . B SF4 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? 
metalc ? metalc8 B SG CYS 196 B CYS 196 1_555 J FE1 F3S . B F3S 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? 
metalc ? metalc9 B SG CYS 217 B CYS 217 1_555 J FE4 F3S . B F3S 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? 
metalc ? metalc10 B SG CYS 223 B CYS 223 1_555 J FE3 F3S . B F3S 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? 
metalc ? metalc11 B SG CYS 227 B CYS 227 1_555 I FE4 SF4 . B SF4 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? 
metalc ? metalc12 B SG CYS 244 B CYS 244 1_555 H FE2 SF4 . B SF4 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? 
metalc ? metalc13 B SG CYS 247 B CYS 247 1_555 H FE1 SF4 . B SF4 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? 
metalc ? metalc14 B SG CYS 259 B CYS 259 1_555 H FE3 SF4 . B SF4 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? 
metalc ? metalc15 B SG CYS 263 B CYS 263 1_555 G FE1 SF4 . B SF4 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? 
metalc ? metalc16 C NE2 HIS 56 C HIS 56 1_555 K FE HEM . C HEM 806 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? 
metalc ? metalc17 C NE2 HIS 66 C HIS 66 1_555 L FE HEM . C HEM 807 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? 
metalc ? metalc18 C NE2 HIS 187 C HIS 187 1_555 L FE HEM . C HEM 807 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? 
metalc ? metalc19 C NE2 HIS 205 C HIS 205 1_555 K FE HEM . C HEM 806 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? 
#
_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     ? 
#
_atom_sites.entry_id                     3IR6 
_atom_sites.fract_transf_matrix[1][1]    0.006488 
_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]    0.00417 
_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]    0.007149 
_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
D 4 GDP A 1 1247 900 GDP GDP . 
E 4 GDP A 1 1248 901 GDP GDP . 
F 5 AGA A 1 1249 309 AGA AGA . 
G 6 SF4 B 1 802 802 SF4 SF4 . 
H 6 SF4 B 1 803 803 SF4 SF4 . 
I 6 SF4 B 1 804 804 SF4 SF4 . 
J 7 F3S B 1 805 805 F3S F3S . 
K 8 HEM C 1 806 806 HEM HEM . 
L 8 HEM C 1 807 807 HEM HEM . 
M 9 HOH A 1 1250 1 HOH HOH . 
M 9 HOH A 2 1251 2 HOH HOH . 
M 9 HOH A 3 1252 5 HOH HOH . 
M 9 HOH A 4 1253 6 HOH HOH . 
M 9 HOH A 5 1254 8 HOH HOH . 
M 9 HOH A 6 1255 9 HOH HOH . 
M 9 HOH A 7 1256 16 HOH HOH . 
M 9 HOH A 8 1257 19 HOH HOH . 
M 9 HOH A 9 1258 20 HOH HOH . 
M 9 HOH A 10 1259 22 HOH HOH . 
M 9 HOH A 11 1260 24 HOH HOH . 
M 9 HOH A 12 1261 27 HOH HOH . 
M 9 HOH A 13 1262 29 HOH HOH . 
M 9 HOH A 14 1263 30 HOH HOH . 
M 9 HOH A 15 1264 31 HOH HOH . 
M 9 HOH A 16 1265 32 HOH HOH . 
M 9 HOH A 17 1266 33 HOH HOH . 
M 9 HOH A 18 1267 34 HOH HOH . 
M 9 HOH A 19 1268 39 HOH HOH . 
M 9 HOH A 20 1269 41 HOH HOH . 
M 9 HOH A 21 1270 43 HOH HOH . 
M 9 HOH A 22 1271 44 HOH HOH . 
M 9 HOH A 23 1272 45 HOH HOH . 
M 9 HOH A 24 1273 47 HOH HOH . 
M 9 HOH A 25 1274 48 HOH HOH . 
M 9 HOH A 26 1275 49 HOH HOH . 
M 9 HOH A 27 1276 50 HOH HOH . 
M 9 HOH A 28 1277 51 HOH HOH . 
M 9 HOH A 29 1278 52 HOH HOH . 
M 9 HOH A 30 1279 53 HOH HOH . 
M 9 HOH A 31 1280 54 HOH HOH . 
M 9 HOH A 32 1281 55 HOH HOH . 
M 9 HOH A 33 1282 56 HOH HOH . 
M 9 HOH A 34 1283 63 HOH HOH . 
M 9 HOH A 35 1284 67 HOH HOH . 
M 9 HOH A 36 1285 68 HOH HOH . 
M 9 HOH A 37 1286 73 HOH HOH . 
M 9 HOH A 38 1287 74 HOH HOH . 
M 9 HOH A 39 1288 75 HOH HOH . 
M 9 HOH A 40 1289 77 HOH HOH . 
M 9 HOH A 41 1290 80 HOH HOH . 
M 9 HOH A 42 1291 82 HOH HOH . 
M 9 HOH A 43 1292 83 HOH HOH . 
N 9 HOH B 1 513 4 HOH HOH . 
N 9 HOH B 2 514 7 HOH HOH . 
N 9 HOH B 3 515 10 HOH HOH . 
N 9 HOH B 4 516 12 HOH HOH . 
N 9 HOH B 5 517 14 HOH HOH . 
N 9 HOH B 6 518 15 HOH HOH . 
N 9 HOH B 7 519 18 HOH HOH . 
N 9 HOH B 8 520 21 HOH HOH . 
N 9 HOH B 9 521 23 HOH HOH . 
N 9 HOH B 10 522 25 HOH HOH . 
N 9 HOH B 11 523 28 HOH HOH . 
N 9 HOH B 12 524 38 HOH HOH . 
N 9 HOH B 13 525 40 HOH HOH . 
N 9 HOH B 14 526 42 HOH HOH . 
N 9 HOH B 15 527 46 HOH HOH . 
N 9 HOH B 16 528 57 HOH HOH . 
N 9 HOH B 17 529 58 HOH HOH . 
N 9 HOH B 18 530 60 HOH HOH . 
N 9 HOH B 19 531 61 HOH HOH . 
N 9 HOH B 20 532 62 HOH HOH . 
N 9 HOH B 21 533 64 HOH HOH . 
N 9 HOH B 22 534 65 HOH HOH . 
N 9 HOH B 23 535 69 HOH HOH . 
N 9 HOH B 24 536 70 HOH HOH . 
N 9 HOH B 25 537 71 HOH HOH . 
N 9 HOH B 26 538 72 HOH HOH . 
N 9 HOH B 27 539 76 HOH HOH . 
N 9 HOH B 28 540 78 HOH HOH . 
N 9 HOH B 29 541 79 HOH HOH . 
O 9 HOH C 1 226 3 HOH HOH . 
O 9 HOH C 2 227 11 HOH HOH . 
O 9 HOH C 3 228 13 HOH HOH . 
O 9 HOH C 4 229 17 HOH HOH . 
O 9 HOH C 5 230 26 HOH HOH . 
O 9 HOH C 6 231 35 HOH HOH . 
O 9 HOH C 7 232 36 HOH HOH . 
O 9 HOH C 8 233 37 HOH HOH . 
O 9 HOH C 9 234 59 HOH HOH . 
O 9 HOH C 10 235 66 HOH HOH . 
O 9 HOH C 11 236 81 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 4 -123.312 -63.089 -24.372 1 56.59 ? PB GDP 1247 A 1 
HETATM 2 O O1B GDP . . . D 4 -123.086 -63.815 -25.646 1 56.59 ? O1B GDP 1247 A 1 
HETATM 3 O O2B GDP . . . D 4 -122.1 -62.609 -23.712 1 56.59 ? O2B GDP 1247 A 1 
HETATM 4 O O3B GDP . . . D 4 -124.183 -64.04 -23.387 1 56.59 ? O3B GDP 1247 A 1 
HETATM 5 O O3A GDP . . . D 4 -124.248 -61.811 -24.62 1 56.59 ? O3A GDP 1247 A 1 
HETATM 6 P PA GDP . . . D 4 -125.273 -60.777 -24.034 1 56.59 ? PA GDP 1247 A 1 
HETATM 7 O O1A GDP . . . D 4 -124.592 -59.991 -23.017 1 56.59 ? O1A GDP 1247 A 1 
HETATM 8 O O2A GDP . . . D 4 -126.511 -61.519 -23.63 1 56.59 ? O2A GDP 1247 A 1 
HETATM 9 O O5' GDP . . . D 4 -125.451 -59.945 -25.401 1 56.59 ? O5' GDP 1247 A 1 
HETATM 10 C C5' GDP . . . D 4 -126.098 -60.155 -26.638 1 56.59 ? C5' GDP 1247 A 1 
HETATM 11 C C4' GDP . . . D 4 -125.569 -59.191 -27.65 1 56.59 ? C4' GDP 1247 A 1 
HETATM 12 O O4' GDP . . . D 4 -126.09 -59.567 -28.913 1 56.59 ? O4' GDP 1247 A 1 
HETATM 13 C C3' GDP . . . D 4 -126.011 -57.763 -27.334 1 56.59 ? C3' GDP 1247 A 1 
HETATM 14 O O3' GDP . . . D 4 -124.934 -56.845 -27.479 1 56.59 ? O3' GDP 1247 A 1 
HETATM 15 C C2' GDP . . . D 4 -127.188 -57.531 -28.292 1 56.59 ? C2' GDP 1247 A 1 
HETATM 16 O O2' GDP . . . D 4 -127.329 -56.146 -28.626 1 56.59 ? O2' GDP 1247 A 1 
HETATM 17 C C1' GDP . . . D 4 -126.863 -58.485 -29.478 1 56.59 ? C1' GDP 1247 A 1 
HETATM 18 N N9 GDP . . . D 4 -128.019 -59.16 -30.096 1 56.59 ? N9 GDP 1247 A 1 
HETATM 19 C C8 GDP . . . D 4 -129.268 -59.51 -29.597 1 56.59 ? C8 GDP 1247 A 1 
HETATM 20 N N7 GDP . . . D 4 -130.059 -60.117 -30.447 1 56.59 ? N7 GDP 1247 A 1 
HETATM 21 C C5 GDP . . . D 4 -129.313 -60.192 -31.595 1 56.59 ? C5 GDP 1247 A 1 
HETATM 22 C C6 GDP . . . D 4 -129.604 -60.75 -32.896 1 56.59 ? C6 GDP 1247 A 1 
HETATM 23 O O6 GDP . . . D 4 -130.669 -61.291 -33.177 1 56.59 ? O6 GDP 1247 A 1 
HETATM 24 N N1 GDP . . . D 4 -128.547 -60.635 -33.86 1 56.59 ? N1 GDP 1247 A 1 
HETATM 25 C C2 GDP . . . D 4 -127.29 -60.031 -33.612 1 56.59 ? C2 GDP 1247 A 1 
HETATM 26 N N2 GDP . . . D 4 -126.434 -60.008 -34.6 1 56.59 ? N2 GDP 1247 A 1 
HETATM 27 N N3 GDP . . . D 4 -126.996 -59.497 -32.376 1 56.59 ? N3 GDP 1247 A 1 
HETATM 28 C C4 GDP . . . D 4 -128.039 -59.604 -31.409 1 56.59 ? C4 GDP 1247 A 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    31 
_model_server_stats.query_time_ms           309 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           28 
#