data_8XHD
#
_model_server_result.job_id            y6mNxYQSED9aq52RAPFvVA 
_model_server_result.datetime_utc      '2024-11-25 15:21:20' 
_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          8xhd 
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_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":501}' 
#
_entry.id    8XHD 
#
_exptl.entry_id    8XHD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              378.272 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-glutamic acid' 
_entity.pdbx_number_of_molecules    1 
_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         120 
_cell.entry_id            8XHD 
_cell.length_a            117.734 
_cell.length_b            117.734 
_cell.length_c            145.018 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8XHD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        154 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 32 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C13 H19 N2 O9 P' 
_chem_comp.formula_weight    378.272 
_chem_comp.id                PGU 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-glutamic acid' 
_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
O1P P PGU doub 237 n n 
CA CB PGU sing 238 n n 
CA C PGU sing 239 n n 
CA N PGU sing 240 n n 
OXT C PGU doub 241 n n 
CB CG PGU sing 242 n n 
O2P P PGU sing 243 n n 
C O PGU sing 244 n n 
C4A N PGU sing 245 n n 
C4A C4 PGU sing 246 n n 
O3 C3 PGU sing 247 n n 
P O4P PGU sing 248 n n 
P O3P PGU sing 249 n n 
O4P C5A PGU sing 250 n n 
C3 C4 PGU doub 251 n y 
C3 C2 PGU sing 252 n y 
C4 C5 PGU sing 253 n y 
CG CD PGU sing 254 n n 
C2 C2A PGU sing 255 n n 
C2 N1 PGU doub 256 n y 
C5 C5A PGU sing 257 n n 
C5 C6 PGU doub 258 n y 
N1 C6 PGU sing 259 n y 
CD OE2 PGU doub 260 n n 
CD OE1 PGU sing 261 n n 
C2A H2A1 PGU sing 262 n n 
C2A H2A2 PGU sing 263 n n 
C2A H2A3 PGU sing 264 n n 
O3 HO3 PGU sing 265 n n 
C4A H4A1 PGU sing 266 n n 
C4A H4A2 PGU sing 267 n n 
C6 H6 PGU sing 268 n n 
C5A H5A1 PGU sing 269 n n 
C5A H5A2 PGU sing 270 n n 
O2P HO2P PGU sing 271 n n 
O3P HO3P PGU sing 272 n n 
N HN PGU sing 273 n n 
CA HA PGU sing 274 n n 
CB HB1 PGU sing 275 n n 
CB HB2 PGU sing 276 n n 
CG HG1 PGU sing 277 n n 
CG HG2 PGU sing 278 n n 
OE1 HOE1 PGU sing 279 n n 
O HO PGU sing 280 n n 
#
_atom_sites.entry_id                     8XHD 
_atom_sites.fract_transf_matrix[1][1]    0.008494 
_atom_sites.fract_transf_matrix[1][2]    0.004904 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009808 
_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]    0.006896 
_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
C 2 PGU A 1 501 501 PGU PGU . 
D 3 PLP B 1 501 501 PLP PLP . 
E 4 HOH A 1 601 21 HOH HOH . 
E 4 HOH A 2 602 23 HOH HOH . 
E 4 HOH A 3 603 6 HOH HOH . 
E 4 HOH A 4 604 2 HOH HOH . 
E 4 HOH A 5 605 20 HOH HOH . 
E 4 HOH A 6 606 28 HOH HOH . 
E 4 HOH A 7 607 16 HOH HOH . 
E 4 HOH A 8 608 18 HOH HOH . 
E 4 HOH A 9 609 7 HOH HOH . 
E 4 HOH A 10 610 29 HOH HOH . 
E 4 HOH A 11 611 10 HOH HOH . 
E 4 HOH A 12 612 30 HOH HOH . 
E 4 HOH A 13 613 31 HOH HOH . 
F 4 HOH B 1 601 19 HOH HOH . 
F 4 HOH B 2 602 22 HOH HOH . 
F 4 HOH B 3 603 5 HOH HOH . 
F 4 HOH B 4 604 14 HOH HOH . 
F 4 HOH B 5 605 1 HOH HOH . 
F 4 HOH B 6 606 26 HOH HOH . 
F 4 HOH B 7 607 9 HOH HOH . 
F 4 HOH B 8 608 13 HOH HOH . 
F 4 HOH B 9 609 3 HOH HOH . 
F 4 HOH B 10 610 8 HOH HOH . 
F 4 HOH B 11 611 15 HOH HOH . 
F 4 HOH B 12 612 4 HOH HOH . 
F 4 HOH B 13 613 27 HOH HOH . 
F 4 HOH B 14 614 25 HOH HOH . 
F 4 HOH B 15 615 17 HOH HOH . 
F 4 HOH B 16 616 11 HOH HOH . 
F 4 HOH B 17 617 32 HOH HOH . 
F 4 HOH B 18 618 24 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 N N1 PGU . . . C 2 37.746 -24.24 -5.126 1 58.63 ? N1 PGU 501 A 1 
HETATM 2 C C2 PGU . . . C 2 37.121 -25.41 -5.008 1 60.56 ? C2 PGU 501 A 1 
HETATM 3 C C2A PGU . . . C 2 36.259 -25.651 -3.808 1 57.36 ? C2A PGU 501 A 1 
HETATM 4 C C3 PGU . . . C 2 37.265 -26.399 -5.99 1 65.36 ? C3 PGU 501 A 1 
HETATM 5 O O3 PGU . . . C 2 36.612 -27.586 -5.841 1 64.44 ? O3 PGU 501 A 1 
HETATM 6 C C4 PGU . . . C 2 38.081 -26.159 -7.101 1 63.61 ? C4 PGU 501 A 1 
HETATM 7 C C4A PGU . . . C 2 38.246 -27.2 -8.182 1 63.73 ? C4A PGU 501 A 1 
HETATM 8 C C5 PGU . . . C 2 38.724 -24.917 -7.208 1 57.9 ? C5 PGU 501 A 1 
HETATM 9 C C6 PGU . . . C 2 38.525 -24 -6.193 1 54.2 ? C6 PGU 501 A 1 
HETATM 10 C C5A PGU . . . C 2 39.603 -24.601 -8.379 1 55.73 ? C5A PGU 501 A 1 
HETATM 11 O O4P PGU . . . C 2 38.835 -23.978 -9.456 1 59.69 ? O4P PGU 501 A 1 
HETATM 12 P P PGU . . . C 2 39.456 -23.855 -10.941 1 55.31 ? P PGU 501 A 1 
HETATM 13 O O1P PGU . . . C 2 38.639 -22.786 -11.646 1 51.96 ? O1P PGU 501 A 1 
HETATM 14 O O2P PGU . . . C 2 40.902 -23.453 -10.733 1 53.18 ? O2P PGU 501 A 1 
HETATM 15 O O3P PGU . . . C 2 39.305 -25.223 -11.578 1 55.57 ? O3P PGU 501 A 1 
HETATM 16 N N PGU . . . C 2 38.012 -28.577 -7.73 1 69.04 ? N PGU 501 A 1 
HETATM 17 C CA PGU . . . C 2 37.474 -29.481 -8.772 1 77.23 ? CA PGU 501 A 1 
HETATM 18 C CB PGU . . . C 2 38.538 -29.826 -9.822 1 65.71 ? CB PGU 501 A 1 
HETATM 19 C CG PGU . . . C 2 38.455 -28.959 -11.069 1 63.36 ? CG PGU 501 A 1 
HETATM 20 C CD PGU . . . C 2 39.102 -29.544 -12.312 1 60.74 ? CD PGU 501 A 1 
HETATM 21 O OE1 PGU . . . C 2 40.29 -29.922 -12.242 1 54.62 ? OE1 PGU 501 A 1 
HETATM 22 O OE2 PGU . . . C 2 38.415 -29.614 -13.351 1 67.08 ? OE2 PGU 501 A 1 
HETATM 23 C C PGU . . . C 2 36.879 -30.781 -8.204 1 74.23 ? C PGU 501 A 1 
HETATM 24 O O PGU . . . C 2 37.666 -31.59 -7.672 1 83.02 ? O PGU 501 A 1 
HETATM 25 O OXT PGU . . . C 2 35.649 -30.934 -8.317 1 69.7 ? OXT PGU 501 A 1 
#
_model_server_stats.io_time_ms              62 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           283 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           25 
#