data_5VBZ
#
_model_server_result.job_id            4MXtiKWwad302JkwLJx-SQ 
_model_server_result.datetime_utc      '2024-11-05 05:46:57' 
_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          5vbz 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":302}' 
#
_entry.id    5VBZ 
#
_exptl.entry_id    5VBZ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              522.196 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' 
_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            5VBZ 
_cell.length_a            61.84 
_cell.length_b            75.44 
_cell.length_c            93.63 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5VBZ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
PISA monomeric 1 author_and_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,D,E,K 1 1 
B,F,G,L 2 1 
C,H,I,J,M 3 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
? 2 D N N 
? 2 F N N 
? 2 I 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 SG CYS 77 C CYS 72 1_555 H S24 92V . C 92V 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? 
metalc ? metalc1 A OG SER 22 A SER 17 1_555 E MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? 
metalc ? metalc2 A OG1 THR 40 A THR 35 1_555 E MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? 
metalc ? metalc3 D O1G GNP . A GNP 201 1_555 E MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.853 ? 
metalc ? metalc4 D O1B GNP . A GNP 201 1_555 E MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? 
metalc ? metalc5 E MG MG . A MG 202 1_555 K O HOH . A HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? 
metalc ? metalc6 E MG MG . A MG 202 1_555 K O HOH . A HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? 
metalc ? metalc7 B OG SER 22 B SER 17 1_555 G MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? 
metalc ? metalc8 F O3G GNP . B GNP 201 1_555 G MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? 
metalc ? metalc9 F O2B GNP . B GNP 201 1_555 G MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? 
metalc ? metalc10 G MG MG . B MG 202 1_555 L O HOH . B HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? 
metalc ? metalc11 G MG MG . B MG 202 1_555 L O HOH . B HOH 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
metalc ? metalc12 G MG MG . B MG 202 1_555 L O HOH . B HOH 316 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? 
metalc ? metalc13 C OG SER 22 C SER 17 1_555 J MG MG . C MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? 
metalc ? metalc14 C O THR 40 C THR 35 1_555 J MG MG . C MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? 
metalc ? metalc15 C OG1 THR 40 C THR 35 1_555 J MG MG . C MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? 
metalc ? metalc16 I O3G GNP . C GNP 302 1_555 J MG MG . C MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.866 ? 
metalc ? metalc17 I O2B GNP . C GNP 302 1_555 J MG MG . C MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? 
metalc ? metalc18 J MG MG . C MG 303 1_555 M O HOH . C HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? 
#
_chem_comp.formula           'C10 H17 N6 O13 P3' 
_chem_comp.formula_weight    522.196 
_chem_comp.id                GNP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' 
_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 GNP doub 170 n n 
PG O2G GNP sing 171 n n 
PG O3G GNP sing 172 n n 
PG N3B GNP sing 173 n n 
O2G HOG2 GNP sing 174 n n 
O3G HOG3 GNP sing 175 n n 
N3B PB GNP sing 176 n n 
N3B HNB3 GNP sing 177 n n 
PB O1B GNP doub 178 n n 
PB O2B GNP sing 179 n n 
PB O3A GNP sing 180 n n 
O2B HOB2 GNP sing 181 n n 
O3A PA GNP sing 182 n n 
PA O1A GNP doub 183 n n 
PA O2A GNP sing 184 n n 
PA O5' GNP sing 185 n n 
O2A HOA2 GNP sing 186 n n 
O5' C5' GNP sing 187 n n 
C5' C4' GNP sing 188 n n 
C5' "H5'2" GNP sing 189 n n 
C5' "H5'1" GNP sing 190 n n 
C4' O4' GNP sing 191 n n 
C4' C3' GNP sing 192 n n 
C4' H4' GNP sing 193 n n 
O4' C1' GNP sing 194 n n 
C3' O3' GNP sing 195 n n 
C3' C2' GNP sing 196 n n 
C3' H3' GNP sing 197 n n 
O3' HO3' GNP sing 198 n n 
C2' O2' GNP sing 199 n n 
C2' C1' GNP sing 200 n n 
C2' H2' GNP sing 201 n n 
O2' HO2' GNP sing 202 n n 
C1' N9 GNP sing 203 n n 
C1' H1' GNP sing 204 n n 
N9 C8 GNP sing 205 n y 
N9 C4 GNP sing 206 n y 
C8 N7 GNP doub 207 n y 
C8 H8 GNP sing 208 n n 
N7 C5 GNP sing 209 n y 
C5 C6 GNP sing 210 n y 
C5 C4 GNP doub 211 n y 
C6 O6 GNP doub 212 n n 
C6 N1 GNP sing 213 n y 
N1 C2 GNP sing 214 n y 
N1 HN1 GNP sing 215 n n 
C2 N2 GNP sing 216 n n 
C2 N3 GNP doub 217 n y 
N2 HN21 GNP sing 218 n n 
N2 HN22 GNP sing 219 n n 
N3 C4 GNP sing 220 n y 
#
_atom_sites.entry_id                     5VBZ 
_atom_sites.fract_transf_matrix[1][1]    0.016171 
_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]    0.013256 
_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]    0.01068 
_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 2 GNP A 1 201 2 GNP GNP . 
E 3 MG A 1 202 2 MG MG . 
F 2 GNP B 1 201 1 GNP GNP . 
G 3 MG B 1 202 1 MG MG . 
H 4 92V C 1 301 301 92V LIG . 
I 2 GNP C 1 302 3 GNP GNP . 
J 3 MG C 1 303 3 MG MG . 
K 5 HOH A 1 301 9 HOH HOH . 
K 5 HOH A 2 302 54 HOH HOH . 
K 5 HOH A 3 303 55 HOH HOH . 
K 5 HOH A 4 304 56 HOH HOH . 
K 5 HOH A 5 305 18 HOH HOH . 
K 5 HOH A 6 306 53 HOH HOH . 
K 5 HOH A 7 307 8 HOH HOH . 
K 5 HOH A 8 308 28 HOH HOH . 
K 5 HOH A 9 309 25 HOH HOH . 
K 5 HOH A 10 310 27 HOH HOH . 
K 5 HOH A 11 311 1 HOH HOH . 
K 5 HOH A 12 312 42 HOH HOH . 
K 5 HOH A 13 313 21 HOH HOH . 
K 5 HOH A 14 314 7 HOH HOH . 
K 5 HOH A 15 315 43 HOH HOH . 
K 5 HOH A 16 316 23 HOH HOH . 
K 5 HOH A 17 317 22 HOH HOH . 
K 5 HOH A 18 318 62 HOH HOH . 
K 5 HOH A 19 319 19 HOH HOH . 
K 5 HOH A 20 320 41 HOH HOH . 
K 5 HOH A 21 321 17 HOH HOH . 
K 5 HOH A 22 322 51 HOH HOH . 
L 5 HOH B 1 301 33 HOH HOH . 
L 5 HOH B 2 302 50 HOH HOH . 
L 5 HOH B 3 303 46 HOH HOH . 
L 5 HOH B 4 304 31 HOH HOH . 
L 5 HOH B 5 305 61 HOH HOH . 
L 5 HOH B 6 306 24 HOH HOH . 
L 5 HOH B 7 307 11 HOH HOH . 
L 5 HOH B 8 308 10 HOH HOH . 
L 5 HOH B 9 309 63 HOH HOH . 
L 5 HOH B 10 310 47 HOH HOH . 
L 5 HOH B 11 311 49 HOH HOH . 
L 5 HOH B 12 312 58 HOH HOH . 
L 5 HOH B 13 313 32 HOH HOH . 
L 5 HOH B 14 314 13 HOH HOH . 
L 5 HOH B 15 315 44 HOH HOH . 
L 5 HOH B 16 316 48 HOH HOH . 
M 5 HOH C 1 401 3 HOH HOH . 
M 5 HOH C 2 402 36 HOH HOH . 
M 5 HOH C 3 403 2 HOH HOH . 
M 5 HOH C 4 404 14 HOH HOH . 
M 5 HOH C 5 405 6 HOH HOH . 
M 5 HOH C 6 406 57 HOH HOH . 
M 5 HOH C 7 407 60 HOH HOH . 
M 5 HOH C 8 408 66 HOH HOH . 
M 5 HOH C 9 409 39 HOH HOH . 
M 5 HOH C 10 410 37 HOH HOH . 
M 5 HOH C 11 411 29 HOH HOH . 
M 5 HOH C 12 412 40 HOH HOH . 
M 5 HOH C 13 413 26 HOH HOH . 
M 5 HOH C 14 414 52 HOH HOH . 
M 5 HOH C 15 415 20 HOH HOH . 
M 5 HOH C 16 416 15 HOH HOH . 
M 5 HOH C 17 417 35 HOH HOH . 
M 5 HOH C 18 418 4 HOH HOH . 
M 5 HOH C 19 419 30 HOH HOH . 
M 5 HOH C 20 420 38 HOH HOH . 
M 5 HOH C 21 421 45 HOH HOH . 
M 5 HOH C 22 422 59 HOH HOH . 
M 5 HOH C 23 423 34 HOH HOH . 
M 5 HOH C 24 424 64 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 GNP . . . I 2 -8.281 20.373 -12.44 1 28.24 ? PG GNP 302 C 1 
HETATM 2 O O1G GNP . . . I 2 -7.83 21.175 -13.451 1 28.58 ? O1G GNP 302 C 1 
HETATM 3 O O2G GNP . . . I 2 -7.053 19.668 -11.911 1 26.85 -1 O2G GNP 302 C 1 
HETATM 4 O O3G GNP . . . I 2 -9.07 21.06 -11.287 1 21.56 -1 O3G GNP 302 C 1 
HETATM 5 N N3B GNP . . . I 2 -9.411 19.383 -13.257 1 27.12 ? N3B GNP 302 C 1 
HETATM 6 P PB GNP . . . I 2 -10.331 18.24 -12.415 1 18.19 ? PB GNP 302 C 1 
HETATM 7 O O1B GNP . . . I 2 -9.54 17.231 -11.995 1 11.5 ? O1B GNP 302 C 1 
HETATM 8 O O2B GNP . . . I 2 -10.935 19.024 -11.293 1 19.23 -1 O2B GNP 302 C 1 
HETATM 9 O O3A GNP . . . I 2 -11.387 17.771 -13.435 1 14.6 ? O3A GNP 302 C 1 
HETATM 10 P PA GNP . . . I 2 -12.835 18.293 -13.672 1 17.28 ? PA GNP 302 C 1 
HETATM 11 O O1A GNP . . . I 2 -12.831 19.697 -13.824 1 18.29 -1 O1A GNP 302 C 1 
HETATM 12 O O2A GNP . . . I 2 -13.645 17.862 -12.626 1 19.29 ? O2A GNP 302 C 1 
HETATM 13 O O5' GNP . . . I 2 -13.281 17.668 -14.994 1 16.74 ? O5' GNP 302 C 1 
HETATM 14 C C5' GNP . . . I 2 -12.425 17.474 -16.087 1 18.89 ? C5' GNP 302 C 1 
HETATM 15 C C4' GNP . . . I 2 -13.133 17.064 -17.358 1 21.09 ? C4' GNP 302 C 1 
HETATM 16 O O4' GNP . . . I 2 -13.561 15.74 -17.382 1 19.3 ? O4' GNP 302 C 1 
HETATM 17 C C3' GNP . . . I 2 -14.355 17.932 -17.582 1 20.46 ? C3' GNP 302 C 1 
HETATM 18 O O3' GNP . . . I 2 -14.329 18.312 -18.935 1 20.97 ? O3' GNP 302 C 1 
HETATM 19 C C2' GNP . . . I 2 -15.502 17.054 -17.193 1 20.65 ? C2' GNP 302 C 1 
HETATM 20 O O2' GNP . . . I 2 -16.642 17.246 -17.964 1 23.08 ? O2' GNP 302 C 1 
HETATM 21 C C1' GNP . . . I 2 -14.951 15.659 -17.409 1 18.9 ? C1' GNP 302 C 1 
HETATM 22 N N9 GNP . . . I 2 -15.358 14.647 -16.453 1 13.24 ? N9 GNP 302 C 1 
HETATM 23 C C8 GNP . . . I 2 -15.137 14.624 -15.193 1 14.48 ? C8 GNP 302 C 1 
HETATM 24 N N7 GNP . . . I 2 -15.577 13.55 -14.653 1 14.62 ? N7 GNP 302 C 1 
HETATM 25 C C5 GNP . . . I 2 -16.114 12.841 -15.59 1 14.34 ? C5 GNP 302 C 1 
HETATM 26 C C6 GNP . . . I 2 -16.778 11.571 -15.675 1 15.74 ? C6 GNP 302 C 1 
HETATM 27 O O6 GNP . . . I 2 -16.937 10.914 -14.697 1 17.02 ? O6 GNP 302 C 1 
HETATM 28 N N1 GNP . . . I 2 -17.187 11.185 -16.85 1 16.93 ? N1 GNP 302 C 1 
HETATM 29 C C2 GNP . . . I 2 -16.988 11.914 -17.954 1 17.4 ? C2 GNP 302 C 1 
HETATM 30 N N2 GNP . . . I 2 -17.398 11.504 -19.137 1 18.51 ? N2 GNP 302 C 1 
HETATM 31 N N3 GNP . . . I 2 -16.401 13.099 -17.921 1 16.15 ? N3 GNP 302 C 1 
HETATM 32 C C4 GNP . . . I 2 -15.955 13.578 -16.792 1 13.32 ? C4 GNP 302 C 1 
HETATM 33 H HNB3 GNP . . . I 2 -9.547 19.505 -14.243 1 32.54 ? HNB3 GNP 302 C 1 
HETATM 34 H "H5'2" GNP . . . I 2 -11.724 16.694 -15.819 1 22.67 ? "H5'2" GNP 302 C 1 
HETATM 35 H "H5'1" GNP . . . I 2 -11.842 18.365 -16.282 1 22.67 ? "H5'1" GNP 302 C 1 
HETATM 36 H H4' GNP . . . I 2 -12.441 17.209 -18.185 1 25.3 ? H4' GNP 302 C 1 
HETATM 37 H H3' GNP . . . I 2 -14.323 18.794 -16.917 1 24.56 ? H3' GNP 302 C 1 
HETATM 38 H HO3' GNP . . . I 2 -14.973 17.82 -19.443 1 25.17 ? HO3' GNP 302 C 1 
HETATM 39 H H2' GNP . . . I 2 -15.719 17.211 -16.138 1 24.78 ? H2' GNP 302 C 1 
HETATM 40 H HO2' GNP . . . I 2 -17.302 17.718 -17.458 1 27.69 ? HO2' GNP 302 C 1 
HETATM 41 H H1' GNP . . . I 2 -15.246 15.326 -18.403 1 22.68 ? H1' GNP 302 C 1 
HETATM 42 H H8 GNP . . . I 2 -14.639 15.407 -14.653 1 17.38 ? H8 GNP 302 C 1 
HETATM 43 H HN1 GNP . . . I 2 -17.658 10.268 -16.924 1 20.32 ? HN1 GNP 302 C 1 
HETATM 44 H HN21 GNP . . . I 2 -17.238 12.089 -19.929 1 22.21 ? HN21 GNP 302 C 1 
HETATM 45 H HN22 GNP . . . I 2 -17.874 10.631 -19.255 1 22.21 ? HN22 GNP 302 C 1 
#
_model_server_stats.io_time_ms              20 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    16 
_model_server_stats.query_time_ms           360 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           45 
#