data_6KYK
#
_model_server_result.job_id            N5zClp-G3huLcXXM1EG0lA 
_model_server_result.datetime_utc      '2024-10-19 10:17:49' 
_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          6kyk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":201}' 
#
_entry.id    6KYK 
#
_exptl.entry_id    6KYK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              522.196 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          109.51 
_cell.angle_gamma         90 
_cell.entry_id            6KYK 
_cell.length_a            171.032 
_cell.length_b            54.107 
_cell.length_c            203.11 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6KYK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 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
? trimeric 3 author_defined_assembly 1 
? trimeric 3 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,G,H,I,J,O,Q,R 1 1 
B,E,F,K,L,M,N,P,S,T 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 G N N 
? 3 I N N 
? 3 K N N 
? 3 M 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
disulf ? disulf1 A SG CYS 264 A CYS 258 1_555 A SG CYS 296 A CYS 290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? 
disulf ? disulf2 B SG CYS 264 B CYS 258 1_555 B SG CYS 296 B CYS 290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? 
metalc ? metalc1 C OG1 THR 38 C THR 35 1_555 H MG MG . C MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.732 ? 
metalc ? metalc2 G O3G GNP . C GNP 201 1_555 H MG MG . C MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? 
metalc ? metalc3 G O2B GNP . C GNP 201 1_555 H MG MG . C MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? 
metalc ? metalc4 H MG MG . C MG 202 1_555 Q O HOH . C HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.596 ? 
metalc ? metalc5 H MG MG . C MG 202 1_555 Q O HOH . C HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.944 ? 
metalc ? metalc6 I O3G GNP . D GNP 201 1_555 J MG MG . D MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? 
metalc ? metalc7 I O2B GNP . D GNP 201 1_555 J MG MG . D MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
metalc ? metalc8 J MG MG . D MG 202 1_555 R O HOH . D HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? 
metalc ? metalc9 J MG MG . D MG 202 1_555 R O HOH . D HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? 
metalc ? metalc10 E OG1 THR 38 E THR 35 1_555 L MG MG . E MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? 
metalc ? metalc11 K O3G GNP . E GNP 201 1_555 L MG MG . E MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? 
metalc ? metalc12 K O2B GNP . E GNP 201 1_555 L MG MG . E MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? 
metalc ? metalc13 L MG MG . E MG 202 1_555 S O HOH . E HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? 
metalc ? metalc14 L MG MG . E MG 202 1_555 S O HOH . E HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.981 ? 
metalc ? metalc15 F OG1 THR 38 F THR 35 1_555 N MG MG . F MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.77 ? 
metalc ? metalc16 M O3G GNP . F GNP 201 1_555 N MG MG . F MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? 
metalc ? metalc17 M O2B GNP . F GNP 201 1_555 N MG MG . F MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? 
metalc ? metalc18 N MG MG . F MG 202 1_555 T O HOH . F HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.437 ? 
#
_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 129 n n 
PG O2G GNP sing 130 n n 
PG O3G GNP sing 131 n n 
PG N3B GNP sing 132 n n 
O2G HOG2 GNP sing 133 n n 
O3G HOG3 GNP sing 134 n n 
N3B PB GNP sing 135 n n 
N3B HNB3 GNP sing 136 n n 
PB O1B GNP doub 137 n n 
PB O2B GNP sing 138 n n 
PB O3A GNP sing 139 n n 
O2B HOB2 GNP sing 140 n n 
O3A PA GNP sing 141 n n 
PA O1A GNP doub 142 n n 
PA O2A GNP sing 143 n n 
PA O5' GNP sing 144 n n 
O2A HOA2 GNP sing 145 n n 
O5' C5' GNP sing 146 n n 
C5' C4' GNP sing 147 n n 
C5' "H5'2" GNP sing 148 n n 
C5' "H5'1" GNP sing 149 n n 
C4' O4' GNP sing 150 n n 
C4' C3' GNP sing 151 n n 
C4' H4' GNP sing 152 n n 
O4' C1' GNP sing 153 n n 
C3' O3' GNP sing 154 n n 
C3' C2' GNP sing 155 n n 
C3' H3' GNP sing 156 n n 
O3' HO3' GNP sing 157 n n 
C2' O2' GNP sing 158 n n 
C2' C1' GNP sing 159 n n 
C2' H2' GNP sing 160 n n 
O2' HO2' GNP sing 161 n n 
C1' N9 GNP sing 162 n n 
C1' H1' GNP sing 163 n n 
N9 C8 GNP sing 164 n y 
N9 C4 GNP sing 165 n y 
C8 N7 GNP doub 166 n y 
C8 H8 GNP sing 167 n n 
N7 C5 GNP sing 168 n y 
C5 C6 GNP sing 169 n y 
C5 C4 GNP doub 170 n y 
C6 O6 GNP doub 171 n n 
C6 N1 GNP sing 172 n y 
N1 C2 GNP sing 173 n y 
N1 HN1 GNP sing 174 n n 
C2 N2 GNP sing 175 n n 
C2 N3 GNP doub 176 n y 
N2 HN21 GNP sing 177 n n 
N2 HN22 GNP sing 178 n n 
N3 C4 GNP sing 179 n y 
#
_atom_sites.entry_id                     6KYK 
_atom_sites.fract_transf_matrix[1][1]    0.005847 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002072 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.018482 
_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]    0.005223 
_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 3 GNP C 1 201 201 GNP GNP . 
H 4 MG C 1 202 202 MG MG . 
I 3 GNP D 1 201 201 GNP GNP . 
J 4 MG D 1 202 202 MG MG . 
K 3 GNP E 1 201 201 GNP GNP . 
L 4 MG E 1 202 202 MG MG . 
M 3 GNP F 1 201 201 GNP GNP . 
N 4 MG F 1 202 202 MG MG . 
O 5 HOH A 1 401 58 HOH HOH . 
O 5 HOH A 2 402 62 HOH HOH . 
O 5 HOH A 3 403 35 HOH HOH . 
O 5 HOH A 4 404 23 HOH HOH . 
O 5 HOH A 5 405 66 HOH HOH . 
O 5 HOH A 6 406 49 HOH HOH . 
O 5 HOH A 7 407 69 HOH HOH . 
O 5 HOH A 8 408 31 HOH HOH . 
O 5 HOH A 9 409 60 HOH HOH . 
O 5 HOH A 10 410 54 HOH HOH . 
O 5 HOH A 11 411 29 HOH HOH . 
O 5 HOH A 12 412 25 HOH HOH . 
O 5 HOH A 13 413 55 HOH HOH . 
O 5 HOH A 14 414 61 HOH HOH . 
O 5 HOH A 15 415 68 HOH HOH . 
O 5 HOH A 16 416 26 HOH HOH . 
O 5 HOH A 17 417 41 HOH HOH . 
P 5 HOH B 1 401 8 HOH HOH . 
P 5 HOH B 2 402 18 HOH HOH . 
P 5 HOH B 3 403 32 HOH HOH . 
P 5 HOH B 4 404 27 HOH HOH . 
P 5 HOH B 5 405 42 HOH HOH . 
P 5 HOH B 6 406 11 HOH HOH . 
P 5 HOH B 7 407 48 HOH HOH . 
P 5 HOH B 8 408 65 HOH HOH . 
P 5 HOH B 9 409 45 HOH HOH . 
P 5 HOH B 10 410 51 HOH HOH . 
P 5 HOH B 11 411 9 HOH HOH . 
P 5 HOH B 12 412 20 HOH HOH . 
P 5 HOH B 13 413 47 HOH HOH . 
P 5 HOH B 14 414 64 HOH HOH . 
P 5 HOH B 15 415 50 HOH HOH . 
P 5 HOH B 16 416 12 HOH HOH . 
P 5 HOH B 17 417 52 HOH HOH . 
P 5 HOH B 18 418 19 HOH HOH . 
Q 5 HOH C 1 301 72 HOH HOH . 
Q 5 HOH C 2 302 33 HOH HOH . 
Q 5 HOH C 3 303 73 HOH HOH . 
Q 5 HOH C 4 304 43 HOH HOH . 
Q 5 HOH C 5 305 56 HOH HOH . 
Q 5 HOH C 6 306 44 HOH HOH . 
Q 5 HOH C 7 307 36 HOH HOH . 
Q 5 HOH C 8 308 46 HOH HOH . 
R 5 HOH D 1 301 7 HOH HOH . 
R 5 HOH D 2 302 63 HOH HOH . 
R 5 HOH D 3 303 1 HOH HOH . 
R 5 HOH D 4 304 5 HOH HOH . 
R 5 HOH D 5 305 2 HOH HOH . 
R 5 HOH D 6 306 39 HOH HOH . 
R 5 HOH D 7 307 67 HOH HOH . 
R 5 HOH D 8 308 6 HOH HOH . 
S 5 HOH E 1 301 10 HOH HOH . 
S 5 HOH E 2 302 71 HOH HOH . 
S 5 HOH E 3 303 70 HOH HOH . 
S 5 HOH E 4 304 38 HOH HOH . 
S 5 HOH E 5 305 59 HOH HOH . 
S 5 HOH E 6 306 16 HOH HOH . 
S 5 HOH E 7 307 17 HOH HOH . 
S 5 HOH E 8 308 15 HOH HOH . 
S 5 HOH E 9 309 14 HOH HOH . 
S 5 HOH E 10 310 13 HOH HOH . 
T 5 HOH F 1 301 4 HOH HOH . 
T 5 HOH F 2 302 28 HOH HOH . 
T 5 HOH F 3 303 3 HOH HOH . 
T 5 HOH F 4 304 40 HOH HOH . 
T 5 HOH F 5 305 57 HOH HOH . 
T 5 HOH F 6 306 53 HOH HOH . 
T 5 HOH F 7 307 34 HOH HOH . 
T 5 HOH F 8 308 22 HOH HOH . 
T 5 HOH F 9 309 24 HOH HOH . 
T 5 HOH F 10 310 21 HOH HOH . 
T 5 HOH F 11 311 30 HOH HOH . 
T 5 HOH F 12 312 37 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 . . . G 3 -32.173 -48.677 56.983 1 58.42 ? PG GNP 201 C 1 
HETATM 2 O O1G GNP . . . G 3 -30.671 -48.955 56.96 1 66.03 ? O1G GNP 201 C 1 
HETATM 3 O O2G GNP . . . G 3 -32.818 -49.971 57.443 1 56.07 ? O2G GNP 201 C 1 
HETATM 4 O O3G GNP . . . G 3 -32.432 -47.536 57.937 1 54.73 ? O3G GNP 201 C 1 
HETATM 5 N N3B GNP . . . G 3 -32.726 -48.206 55.522 1 59.71 ? N3B GNP 201 C 1 
HETATM 6 P PB GNP . . . G 3 -33.906 -47.107 55.32 1 54.07 ? PB GNP 201 C 1 
HETATM 7 O O1B GNP . . . G 3 -35.228 -47.804 55.215 1 62.56 ? O1B GNP 201 C 1 
HETATM 8 O O2B GNP . . . G 3 -33.742 -46.044 56.364 1 58.81 ? O2B GNP 201 C 1 
HETATM 9 O O3A GNP . . . G 3 -33.661 -46.25 53.993 1 52.89 ? O3A GNP 201 C 1 
HETATM 10 P PA GNP . . . G 3 -33.492 -44.652 53.952 1 54.66 ? PA GNP 201 C 1 
HETATM 11 O O1A GNP . . . G 3 -32.303 -44.33 54.796 1 51.5 ? O1A GNP 201 C 1 
HETATM 12 O O2A GNP . . . G 3 -34.815 -44.041 54.276 1 55.12 ? O2A GNP 201 C 1 
HETATM 13 O O5' GNP . . . G 3 -33.166 -44.308 52.419 1 57.85 ? O5' GNP 201 C 1 
HETATM 14 C C5' GNP . . . G 3 -32.431 -45.207 51.55 1 59.07 ? C5' GNP 201 C 1 
HETATM 15 C C4' GNP . . . G 3 -32.178 -44.476 50.261 1 58.61 ? C4' GNP 201 C 1 
HETATM 16 O O4' GNP . . . G 3 -33.4 -44.506 49.481 1 56.39 ? O4' GNP 201 C 1 
HETATM 17 C C3' GNP . . . G 3 -31.804 -42.996 50.436 1 62.7 ? C3' GNP 201 C 1 
HETATM 18 O O3' GNP . . . G 3 -30.75 -42.581 49.576 1 64.78 ? O3' GNP 201 C 1 
HETATM 19 C C2' GNP . . . G 3 -33.114 -42.26 50.138 1 65.63 ? C2' GNP 201 C 1 
HETATM 20 O O2' GNP . . . G 3 -32.883 -40.956 49.638 1 70.47 ? O2' GNP 201 C 1 
HETATM 21 C C1' GNP . . . G 3 -33.782 -43.196 49.126 1 68.69 ? C1' GNP 201 C 1 
HETATM 22 N N9 GNP . . . G 3 -35.244 -43.09 49.122 1 77.22 ? N9 GNP 201 C 1 
HETATM 23 C C8 GNP . . . G 3 -36.079 -43.408 50.167 1 78.58 ? C8 GNP 201 C 1 
HETATM 24 N N7 GNP . . . G 3 -37.344 -43.178 49.917 1 77.44 ? N7 GNP 201 C 1 
HETATM 25 C C5 GNP . . . G 3 -37.347 -42.662 48.628 1 80.04 ? C5 GNP 201 C 1 
HETATM 26 C C6 GNP . . . G 3 -38.437 -42.225 47.832 1 82.34 ? C6 GNP 201 C 1 
HETATM 27 O O6 GNP . . . G 3 -39.635 -42.172 48.15 1 71 ? O6 GNP 201 C 1 
HETATM 28 N N1 GNP . . . G 3 -38.003 -41.771 46.579 1 89.21 ? N1 GNP 201 C 1 
HETATM 29 C C2 GNP . . . G 3 -36.695 -41.749 46.149 1 78.92 ? C2 GNP 201 C 1 
HETATM 30 N N2 GNP . . . G 3 -36.464 -41.294 44.909 1 78.43 ? N2 GNP 201 C 1 
HETATM 31 N N3 GNP . . . G 3 -35.671 -42.158 46.898 1 75.46 ? N3 GNP 201 C 1 
HETATM 32 C C4 GNP . . . G 3 -36.063 -42.598 48.123 1 78.66 ? C4 GNP 201 C 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           27 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           308 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           32 
#