data_6YXW
#
_model_server_result.job_id            WO8JHfeU8_ARi2xPjiXFJQ 
_model_server_result.datetime_utc      '2024-11-22 19:42:23' 
_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          6yxw 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":201}' 
#
_entry.id    6YXW 
#
_exptl.entry_id    6YXW 
_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         90 
_cell.angle_beta          106.91 
_cell.angle_gamma         90 
_cell.entry_id            6YXW 
_cell.length_a            73.126 
_cell.length_b            39.49 
_cell.length_c            113.212 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6YXW 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 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
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,E,F,I,J 1 1 
C,D,G,H,K,L 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 E N N 
? 3 G 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 OG SER 20 A SER 17 1_555 F MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? 
metalc ? metalc2 E O2B GDP . A GDP 201 1_555 F MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
metalc ? metalc3 F MG MG . A MG 202 1_555 I O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? 
metalc ? metalc4 F MG MG . A MG 202 1_555 I O HOH . A HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? 
metalc ? metalc5 F MG MG . A MG 202 1_555 I O HOH . A HOH 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? 
metalc ? metalc6 F MG MG . A MG 202 1_555 I O HOH . A HOH 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? 
metalc ? metalc7 C OG SER 20 C SER 17 1_555 H MG MG . C MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? 
metalc ? metalc8 G O1B GDP . C GDP 201 1_555 H MG MG . C MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? 
metalc ? metalc9 H MG MG . C MG 202 1_555 K O HOH . C HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? 
metalc ? metalc10 H MG MG . C MG 202 1_555 K O HOH . C HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? 
metalc ? metalc11 H MG MG . C MG 202 1_555 K O HOH . C HOH 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? 
metalc ? metalc12 H MG MG . C MG 202 1_555 K O HOH . C HOH 322 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? 
#
_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                     6YXW 
_atom_sites.fract_transf_matrix[1][1]    0.013675 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.004158 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.025323 
_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]    0.009232 
_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 3 GDP A 1 201 201 GDP GDP . 
F 4 MG A 1 202 202 MG MG . 
G 3 GDP C 1 201 201 GDP GDP . 
H 4 MG C 1 202 202 MG MG . 
I 5 HOH A 1 301 1 HOH HOH . 
I 5 HOH A 2 302 60 HOH HOH . 
I 5 HOH A 3 303 78 HOH HOH . 
I 5 HOH A 4 304 4 HOH HOH . 
I 5 HOH A 5 305 68 HOH HOH . 
I 5 HOH A 6 306 79 HOH HOH . 
I 5 HOH A 7 307 16 HOH HOH . 
I 5 HOH A 8 308 3 HOH HOH . 
I 5 HOH A 9 309 10 HOH HOH . 
I 5 HOH A 10 310 84 HOH HOH . 
I 5 HOH A 11 311 76 HOH HOH . 
I 5 HOH A 12 312 22 HOH HOH . 
I 5 HOH A 13 313 53 HOH HOH . 
I 5 HOH A 14 314 2 HOH HOH . 
I 5 HOH A 15 315 48 HOH HOH . 
I 5 HOH A 16 316 32 HOH HOH . 
I 5 HOH A 17 317 30 HOH HOH . 
I 5 HOH A 18 318 13 HOH HOH . 
I 5 HOH A 19 319 50 HOH HOH . 
I 5 HOH A 20 320 57 HOH HOH . 
I 5 HOH A 21 321 40 HOH HOH . 
I 5 HOH A 22 322 80 HOH HOH . 
I 5 HOH A 23 323 96 HOH HOH . 
I 5 HOH A 24 324 29 HOH HOH . 
I 5 HOH A 25 325 82 HOH HOH . 
I 5 HOH A 26 326 17 HOH HOH . 
I 5 HOH A 27 327 39 HOH HOH . 
I 5 HOH A 28 328 98 HOH HOH . 
I 5 HOH A 29 329 75 HOH HOH . 
J 5 HOH B 1 201 20 HOH HOH . 
J 5 HOH B 2 202 92 HOH HOH . 
J 5 HOH B 3 203 90 HOH HOH . 
J 5 HOH B 4 204 63 HOH HOH . 
J 5 HOH B 5 205 69 HOH HOH . 
J 5 HOH B 6 206 86 HOH HOH . 
J 5 HOH B 7 207 72 HOH HOH . 
J 5 HOH B 8 208 65 HOH HOH . 
J 5 HOH B 9 209 81 HOH HOH . 
K 5 HOH C 1 301 25 HOH HOH . 
K 5 HOH C 2 302 6 HOH HOH . 
K 5 HOH C 3 303 5 HOH HOH . 
K 5 HOH C 4 304 9 HOH HOH . 
K 5 HOH C 5 305 71 HOH HOH . 
K 5 HOH C 6 306 26 HOH HOH . 
K 5 HOH C 7 307 45 HOH HOH . 
K 5 HOH C 8 308 77 HOH HOH . 
K 5 HOH C 9 309 8 HOH HOH . 
K 5 HOH C 10 310 19 HOH HOH . 
K 5 HOH C 11 311 52 HOH HOH . 
K 5 HOH C 12 312 38 HOH HOH . 
K 5 HOH C 13 313 12 HOH HOH . 
K 5 HOH C 14 314 35 HOH HOH . 
K 5 HOH C 15 315 94 HOH HOH . 
K 5 HOH C 16 316 66 HOH HOH . 
K 5 HOH C 17 317 21 HOH HOH . 
K 5 HOH C 18 318 46 HOH HOH . 
K 5 HOH C 19 319 73 HOH HOH . 
K 5 HOH C 20 320 85 HOH HOH . 
K 5 HOH C 21 321 61 HOH HOH . 
K 5 HOH C 22 322 7 HOH HOH . 
K 5 HOH C 23 323 15 HOH HOH . 
K 5 HOH C 24 324 28 HOH HOH . 
K 5 HOH C 25 325 103 HOH HOH . 
K 5 HOH C 26 326 56 HOH HOH . 
K 5 HOH C 27 327 41 HOH HOH . 
K 5 HOH C 28 328 51 HOH HOH . 
K 5 HOH C 29 329 83 HOH HOH . 
K 5 HOH C 30 330 95 HOH HOH . 
K 5 HOH C 31 331 49 HOH HOH . 
K 5 HOH C 32 332 64 HOH HOH . 
K 5 HOH C 33 333 14 HOH HOH . 
K 5 HOH C 34 334 18 HOH HOH . 
K 5 HOH C 35 335 67 HOH HOH . 
K 5 HOH C 36 336 44 HOH HOH . 
K 5 HOH C 37 337 42 HOH HOH . 
K 5 HOH C 38 338 27 HOH HOH . 
K 5 HOH C 39 339 74 HOH HOH . 
K 5 HOH C 40 340 36 HOH HOH . 
K 5 HOH C 41 341 97 HOH HOH . 
K 5 HOH C 42 342 54 HOH HOH . 
K 5 HOH C 43 343 93 HOH HOH . 
K 5 HOH C 44 344 55 HOH HOH . 
K 5 HOH C 45 345 33 HOH HOH . 
K 5 HOH C 46 346 62 HOH HOH . 
K 5 HOH C 47 347 34 HOH HOH . 
K 5 HOH C 48 348 99 HOH HOH . 
K 5 HOH C 49 349 91 HOH HOH . 
L 5 HOH D 1 201 87 HOH HOH . 
L 5 HOH D 2 202 101 HOH HOH . 
L 5 HOH D 3 203 59 HOH HOH . 
L 5 HOH D 4 204 102 HOH HOH . 
L 5 HOH D 5 205 58 HOH HOH . 
L 5 HOH D 6 206 37 HOH HOH . 
L 5 HOH D 7 207 47 HOH HOH . 
L 5 HOH D 8 208 24 HOH HOH . 
L 5 HOH D 9 209 11 HOH HOH . 
L 5 HOH D 10 210 88 HOH HOH . 
L 5 HOH D 11 211 89 HOH HOH . 
L 5 HOH D 12 212 70 HOH HOH . 
L 5 HOH D 13 213 23 HOH HOH . 
L 5 HOH D 14 214 31 HOH HOH . 
L 5 HOH D 15 215 43 HOH HOH . 
L 5 HOH D 16 216 100 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 . . . G 3 46.666 4.762 -45.51 1 27.69 ? PB GDP 201 C 1 
HETATM 2 O O1B GDP . . . G 3 46.772 3.588 -46.466 1 27.56 ? O1B GDP 201 C 1 
HETATM 3 O O2B GDP . . . G 3 46.907 4.431 -44.057 1 26.75 ? O2B GDP 201 C 1 
HETATM 4 O O3B GDP . . . G 3 45.471 5.639 -45.757 1 29.37 ? O3B GDP 201 C 1 
HETATM 5 O O3A GDP . . . G 3 47.937 5.742 -45.764 1 29.13 ? O3A GDP 201 C 1 
HETATM 6 P PA GDP . . . G 3 48.847 5.867 -47.106 1 29.71 ? PA GDP 201 C 1 
HETATM 7 O O1A GDP . . . G 3 47.92 6.211 -48.263 1 30.35 ? O1A GDP 201 C 1 
HETATM 8 O O2A GDP . . . G 3 49.797 4.717 -47.204 1 28.84 ? O2A GDP 201 C 1 
HETATM 9 O O5' GDP . . . G 3 49.772 7.155 -46.782 1 30.45 ? O5' GDP 201 C 1 
HETATM 10 C C5' GDP . . . G 3 49.197 8.448 -46.577 1 31.31 ? C5' GDP 201 C 1 
HETATM 11 C C4' GDP . . . G 3 50.199 9.528 -46.938 1 32.45 ? C4' GDP 201 C 1 
HETATM 12 O O4' GDP . . . G 3 51.313 9.462 -46.028 1 32.09 ? O4' GDP 201 C 1 
HETATM 13 C C3' GDP . . . G 3 50.799 9.316 -48.307 1 32.8 ? C3' GDP 201 C 1 
HETATM 14 O O3' GDP . . . G 3 51.134 10.567 -48.858 1 34.53 ? O3' GDP 201 C 1 
HETATM 15 C C2' GDP . . . G 3 52.09 8.568 -48.069 1 32.25 ? C2' GDP 201 C 1 
HETATM 16 O O2' GDP . . . G 3 53.079 8.759 -49.086 1 34.03 ? O2' GDP 201 C 1 
HETATM 17 C C1' GDP . . . G 3 52.52 9.178 -46.751 1 31.82 ? C1' GDP 201 C 1 
HETATM 18 N N9 GDP . . . G 3 53.35 8.238 -45.989 1 29.91 ? N9 GDP 201 C 1 
HETATM 19 C C8 GDP . . . G 3 53.078 6.951 -45.736 1 28.09 ? C8 GDP 201 C 1 
HETATM 20 N N7 GDP . . . G 3 54.063 6.424 -44.988 1 27.49 ? N7 GDP 201 C 1 
HETATM 21 C C5 GDP . . . G 3 54.974 7.375 -44.771 1 28.4 ? C5 GDP 201 C 1 
HETATM 22 C C6 GDP . . . G 3 56.258 7.465 -44.053 1 29.01 ? C6 GDP 201 C 1 
HETATM 23 O O6 GDP . . . G 3 56.724 6.472 -43.465 1 28.06 ? O6 GDP 201 C 1 
HETATM 24 N N1 GDP . . . G 3 56.892 8.637 -44.04 1 30.88 ? N1 GDP 201 C 1 
HETATM 25 C C2 GDP . . . G 3 56.406 9.712 -44.677 1 32.34 ? C2 GDP 201 C 1 
HETATM 26 N N2 GDP . . . G 3 57.11 10.856 -44.626 1 34.58 ? N2 GDP 201 C 1 
HETATM 27 N N3 GDP . . . G 3 55.228 9.707 -45.37 1 31.98 ? N3 GDP 201 C 1 
HETATM 28 C C4 GDP . . . G 3 54.49 8.574 -45.424 1 29.98 ? C4 GDP 201 C 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           305 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#