data_5XKF
#
_model_server_result.job_id            XyXAWD7O1nWVOKSHm31y5A 
_model_server_result.datetime_utc      '2024-10-20 19:56:10' 
_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          5xkf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"R","auth_seq_id":501}' 
#
_entry.id    5XKF 
#
_exptl.entry_id    5XKF 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              523.18 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-TRIPHOSPHATE" 
_entity.pdbx_number_of_molecules    3 
_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            5XKF 
_cell.length_a            105.617 
_cell.length_b            158.572 
_cell.length_c            182.245 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5XKF 
_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        ? 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_pdbx_struct_assembly.details               author_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,U,V,W,X,Y 
_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
? 5 G N N 
? 5 O N N 
? 5 R 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.657 ? 
metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.945 ? 
metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.597 ? 
metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.806 ? 
metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.594 ? 
metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.908 ? 
metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.817 ? 
metalc ? metalc8 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? 
metalc ? metalc9 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? 
metalc ? metalc10 H MG MG . A MG 502 1_555 U O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? 
metalc ? metalc11 H MG MG . A MG 502 1_555 U O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
metalc ? metalc12 H MG MG . A MG 502 1_555 U O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.505 ? 
metalc ? metalc13 H MG MG . A MG 502 1_555 V O HOH . B HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? 
metalc ? metalc14 B OE1 GLN 11 B GLN 11 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? 
metalc ? metalc15 K O1A GDP . B GDP 501 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.533 ? 
metalc ? metalc16 L MG MG . B MG 502 1_555 V O HOH . B HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? 
metalc ? metalc17 C OD1 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? 
metalc ? metalc18 C O THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.695 ? 
metalc ? metalc19 C OG1 THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.639 ? 
metalc ? metalc20 C O GLY 44 C GLY 44 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? 
metalc ? metalc21 C OE1 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.944 ? 
metalc ? metalc22 C OE2 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? 
metalc ? metalc23 O O1G GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? 
metalc ? metalc24 O O1B GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? 
metalc ? metalc25 P MG MG . C MG 502 1_555 W O HOH . C HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? 
metalc ? metalc26 P MG MG . C MG 502 1_555 W O HOH . C HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? 
metalc ? metalc27 P MG MG . C MG 502 1_555 W O HOH . C HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? 
metalc ? metalc28 P MG MG . C MG 502 1_555 W O HOH . C HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? 
metalc ? metalc29 R O1G GTP . D GTP 501 1_555 S MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.891 ? 
metalc ? metalc30 R O1B GTP . D GTP 501 1_555 S MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.865 ? 
metalc ? metalc31 S MG MG . D MG 502 1_555 X O HOH . D HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? 
#
_chem_comp.formula           'C10 H16 N5 O14 P3' 
_chem_comp.formula_weight    523.18 
_chem_comp.id                GTP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "GUANOSINE-5'-TRIPHOSPHATE" 
_chem_comp.type              non-polymer 
_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
PG O1G GTP doub 227 n n 
PG O2G GTP sing 228 n n 
PG O3G GTP sing 229 n n 
PG O3B GTP sing 230 n n 
O2G HOG2 GTP sing 231 n n 
O3G HOG3 GTP sing 232 n n 
O3B PB GTP sing 233 n n 
PB O1B GTP doub 234 n n 
PB O2B GTP sing 235 n n 
PB O3A GTP sing 236 n n 
O2B HOB2 GTP sing 237 n n 
O3A PA GTP sing 238 n n 
PA O1A GTP doub 239 n n 
PA O2A GTP sing 240 n n 
PA O5' GTP sing 241 n n 
O2A HOA2 GTP sing 242 n n 
O5' C5' GTP sing 243 n n 
C5' C4' GTP sing 244 n n 
C5' H5' GTP sing 245 n n 
C5' "H5''" GTP sing 246 n n 
C4' O4' GTP sing 247 n n 
C4' C3' GTP sing 248 n n 
C4' H4' GTP sing 249 n n 
O4' C1' GTP sing 250 n n 
C3' O3' GTP sing 251 n n 
C3' C2' GTP sing 252 n n 
C3' H3' GTP sing 253 n n 
O3' HO3' GTP sing 254 n n 
C2' O2' GTP sing 255 n n 
C2' C1' GTP sing 256 n n 
C2' H2' GTP sing 257 n n 
O2' HO2' GTP sing 258 n n 
C1' N9 GTP sing 259 n n 
C1' H1' GTP sing 260 n n 
N9 C8 GTP sing 261 n y 
N9 C4 GTP sing 262 n y 
C8 N7 GTP doub 263 n y 
C8 H8 GTP sing 264 n n 
N7 C5 GTP sing 265 n y 
C5 C6 GTP sing 266 n n 
C5 C4 GTP doub 267 n y 
C6 O6 GTP doub 268 n n 
C6 N1 GTP sing 269 n n 
N1 C2 GTP sing 270 n n 
N1 HN1 GTP sing 271 n n 
C2 N2 GTP sing 272 n n 
C2 N3 GTP doub 273 n n 
N2 HN21 GTP sing 274 n n 
N2 HN22 GTP sing 275 n n 
N3 C4 GTP sing 276 n n 
#
_atom_sites.entry_id                     5XKF 
_atom_sites.fract_transf_matrix[1][1]    0.009468 
_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]    0.006306 
_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]    0.005487 
_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 GOL A 1 504 601 GOL GOL . 
K 9 GDP B 1 501 501 GDP GDP . 
L 6 MG B 1 502 502 MG MG . 
M 10 MES B 1 503 505 MES MES . 
N 11 88U B 1 504 2 88U M68 . 
O 5 GTP C 1 501 501 GTP GTP . 
P 6 MG C 1 502 502 MG MG . 
Q 7 CA C 1 503 504 CA CA . 
R 5 GTP D 1 501 501 GTP GTP . 
S 6 MG D 1 502 502 MG MG . 
T 11 88U D 1 503 1 88U M68 . 
U 12 HOH A 1 601 17 HOH HOH . 
U 12 HOH A 2 602 6 HOH HOH . 
U 12 HOH A 3 603 8 HOH HOH . 
U 12 HOH A 4 604 9 HOH HOH . 
V 12 HOH B 1 601 20 HOH HOH . 
V 12 HOH B 2 602 19 HOH HOH . 
V 12 HOH B 3 603 18 HOH HOH . 
V 12 HOH B 4 604 22 HOH HOH . 
V 12 HOH B 5 605 7 HOH HOH . 
V 12 HOH B 6 606 10 HOH HOH . 
V 12 HOH B 7 607 13 HOH HOH . 
V 12 HOH B 8 608 11 HOH HOH . 
V 12 HOH B 9 609 21 HOH HOH . 
V 12 HOH B 10 610 28 HOH HOH . 
V 12 HOH B 11 611 16 HOH HOH . 
W 12 HOH C 1 601 24 HOH HOH . 
W 12 HOH C 2 602 4 HOH HOH . 
W 12 HOH C 3 603 2 HOH HOH . 
W 12 HOH C 4 604 3 HOH HOH . 
W 12 HOH C 5 605 1 HOH HOH . 
W 12 HOH C 6 606 30 HOH HOH . 
W 12 HOH C 7 607 29 HOH HOH . 
W 12 HOH C 8 608 26 HOH HOH . 
W 12 HOH C 9 609 23 HOH HOH . 
W 12 HOH C 10 610 27 HOH HOH . 
W 12 HOH C 11 611 12 HOH HOH . 
X 12 HOH D 1 601 15 HOH HOH . 
X 12 HOH D 2 602 5 HOH HOH . 
X 12 HOH D 3 603 14 HOH HOH . 
X 12 HOH D 4 604 25 HOH HOH . 
Y 12 HOH E 1 201 31 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 PG GTP . . . R 5 26.698 306.063 -45.127 1 91.16 ? PG GTP 501 D 1 
HETATM 2 O O1G GTP . . . R 5 27.172 307.181 -46.03 1 88.09 ? O1G GTP 501 D 1 
HETATM 3 O O2G GTP . . . R 5 25.392 305.441 -45.566 1 88.44 ? O2G GTP 501 D 1 
HETATM 4 O O3G GTP . . . R 5 27.762 305.051 -44.769 1 88.64 ? O3G GTP 501 D 1 
HETATM 5 O O3B GTP . . . R 5 26.396 306.78 -43.704 1 87.17 ? O3B GTP 501 D 1 
HETATM 6 P PB GTP . . . R 5 25.057 307.628 -43.381 1 81.83 ? PB GTP 501 D 1 
HETATM 7 O O1B GTP . . . R 5 24.652 308.421 -44.601 1 81.4 ? O1B GTP 501 D 1 
HETATM 8 O O2B GTP . . . R 5 25.263 308.338 -42.065 1 85.73 ? O2B GTP 501 D 1 
HETATM 9 O O3A GTP . . . R 5 23.971 306.459 -43.159 1 79.35 ? O3A GTP 501 D 1 
HETATM 10 P PA GTP . . . R 5 22.413 306.746 -42.856 1 76.09 ? PA GTP 501 D 1 
HETATM 11 O O1A GTP . . . R 5 21.593 306.189 -43.997 1 77.97 ? O1A GTP 501 D 1 
HETATM 12 O O2A GTP . . . R 5 22.237 308.201 -42.48 1 74.9 ? O2A GTP 501 D 1 
HETATM 13 O O5' GTP . . . R 5 22.226 305.835 -41.536 1 73.42 ? O5' GTP 501 D 1 
HETATM 14 C C5' GTP . . . R 5 21.592 304.555 -41.536 1 70.01 ? C5' GTP 501 D 1 
HETATM 15 C C4' GTP . . . R 5 20.543 304.525 -40.425 1 68.67 ? C4' GTP 501 D 1 
HETATM 16 O O4' GTP . . . R 5 19.797 305.741 -40.423 1 67.39 ? O4' GTP 501 D 1 
HETATM 17 C C3' GTP . . . R 5 19.533 303.399 -40.584 1 69.22 ? C3' GTP 501 D 1 
HETATM 18 O O3' GTP . . . R 5 19.469 302.684 -39.346 1 69.95 ? O3' GTP 501 D 1 
HETATM 19 C C2' GTP . . . R 5 18.196 304.048 -40.901 1 68.57 ? C2' GTP 501 D 1 
HETATM 20 O O2' GTP . . . R 5 17.122 303.469 -40.147 1 69.61 ? O2' GTP 501 D 1 
HETATM 21 C C1' GTP . . . R 5 18.39 305.502 -40.512 1 65.46 ? C1' GTP 501 D 1 
HETATM 22 N N9 GTP . . . R 5 17.82 306.463 -41.488 1 62.09 ? N9 GTP 501 D 1 
HETATM 23 C C8 GTP . . . R 5 18.258 306.703 -42.742 1 61.14 ? C8 GTP 501 D 1 
HETATM 24 N N7 GTP . . . R 5 17.514 307.667 -43.345 1 60.01 ? N7 GTP 501 D 1 
HETATM 25 C C5 GTP . . . R 5 16.58 308.064 -42.462 1 60.46 ? C5 GTP 501 D 1 
HETATM 26 C C6 GTP . . . R 5 15.464 309.05 -42.438 1 61.43 ? C6 GTP 501 D 1 
HETATM 27 O O6 GTP . . . R 5 15.211 309.764 -43.432 1 61.78 ? O6 GTP 501 D 1 
HETATM 28 N N1 GTP . . . R 5 14.731 309.151 -41.313 1 60.9 ? N1 GTP 501 D 1 
HETATM 29 C C2 GTP . . . R 5 14.966 308.399 -40.215 1 60 ? C2 GTP 501 D 1 
HETATM 30 N N2 GTP . . . R 5 14.175 308.567 -39.129 1 59.4 ? N2 GTP 501 D 1 
HETATM 31 N N3 GTP . . . R 5 15.97 307.477 -40.165 1 59.77 ? N3 GTP 501 D 1 
HETATM 32 C C4 GTP . . . R 5 16.788 307.268 -41.236 1 60.69 ? C4 GTP 501 D 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           25 
_model_server_stats.create_model_time_ms    38 
_model_server_stats.query_time_ms           280 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           32 
#