data_7XEQ
#
_model_server_result.job_id            o5mOW6dNPHwxwW0LVA898g 
_model_server_result.datetime_utc      '2025-01-10 12:54:37' 
_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          7xeq 
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_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":503}' 
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_entry.id    7XEQ 
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_exptl.entry_id    7XEQ 
_exptl.method      'X-RAY DIFFRACTION' 
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_entity.details                     ? 
_entity.formula_weight              350.285 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(2~{S},4~{S})-2-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]-1,3-thiazolidine-4-carboxylic acid' 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
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_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            7XEQ 
_cell.length_a            103.5 
_cell.length_b            103.5 
_cell.length_c            132.6 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
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_symmetry.entry_id                 7XEQ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 21 2' 
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_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 
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_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
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loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C11 H15 N2 O7 P S' 
_chem_comp.formula_weight    350.285 
_chem_comp.id                9YX 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(2~{S},4~{S})-2-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]-1,3-thiazolidine-4-carboxylic 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
OAM PAL 9YX doub 1 n n 
OAN PAL 9YX sing 2 n n 
O C 9YX doub 3 n n 
PAL OAO 9YX sing 4 n n 
PAL OAK 9YX sing 5 n n 
CB CA 9YX sing 6 n n 
CB SAS 9YX sing 7 n n 
CA C 9YX sing 8 n n 
CA N 9YX sing 9 n n 
C OXT 9YX sing 10 n n 
N CAI 9YX sing 11 n n 
CAJ OAK 9YX sing 12 n n 
CAJ CAA 9YX sing 13 n n 
SAS CAI 9YX sing 14 n n 
CAI CAF 9YX sing 15 n n 
CAA CAF 9YX doub 16 n y 
CAA CAB 9YX sing 17 n y 
CAF CAE 9YX sing 18 n y 
CAB NAC 9YX doub 19 n y 
CAE OAH 9YX sing 20 n n 
CAE CAD 9YX doub 21 n y 
NAC CAD 9YX sing 22 n y 
CAD CAG 9YX sing 23 n n 
OAO H1 9YX sing 24 n n 
OAN H2 9YX sing 25 n n 
CAJ H3 9YX sing 26 n n 
CAJ H4 9YX sing 27 n n 
CAB H5 9YX sing 28 n n 
CAG H6 9YX sing 29 n n 
CAG H7 9YX sing 30 n n 
CAG H8 9YX sing 31 n n 
OAH H9 9YX sing 32 n n 
CAI H10 9YX sing 33 n n 
N H11 9YX sing 34 n n 
CB H13 9YX sing 35 n n 
CB H14 9YX sing 36 n n 
CA H15 9YX sing 37 n n 
OXT H16 9YX sing 38 n n 
#
_atom_sites.entry_id                     7XEQ 
_atom_sites.fract_transf_matrix[1][1]    0.009662 
_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]    0.009662 
_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]    0.007541 
_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
B 2 IPA A 1 501 502 IPA IPA . 
C 3 CL A 1 502 503 CL CL . 
D 4 9YX A 1 503 601 9YX 9YX . 
E 5 HOH A 1 601 13 HOH HOH . 
E 5 HOH A 2 602 44 HOH HOH . 
E 5 HOH A 3 603 25 HOH HOH . 
E 5 HOH A 4 604 26 HOH HOH . 
E 5 HOH A 5 605 36 HOH HOH . 
E 5 HOH A 6 606 9 HOH HOH . 
E 5 HOH A 7 607 23 HOH HOH . 
E 5 HOH A 8 608 16 HOH HOH . 
E 5 HOH A 9 609 1 HOH HOH . 
E 5 HOH A 10 610 19 HOH HOH . 
E 5 HOH A 11 611 29 HOH HOH . 
E 5 HOH A 12 612 35 HOH HOH . 
E 5 HOH A 13 613 43 HOH HOH . 
E 5 HOH A 14 614 49 HOH HOH . 
E 5 HOH A 15 615 6 HOH HOH . 
E 5 HOH A 16 616 47 HOH HOH . 
E 5 HOH A 17 617 12 HOH HOH . 
E 5 HOH A 18 618 55 HOH HOH . 
E 5 HOH A 19 619 28 HOH HOH . 
E 5 HOH A 20 620 27 HOH HOH . 
E 5 HOH A 21 621 14 HOH HOH . 
E 5 HOH A 22 622 42 HOH HOH . 
E 5 HOH A 23 623 8 HOH HOH . 
E 5 HOH A 24 624 41 HOH HOH . 
E 5 HOH A 25 625 34 HOH HOH . 
E 5 HOH A 26 626 18 HOH HOH . 
E 5 HOH A 27 627 21 HOH HOH . 
E 5 HOH A 28 628 7 HOH HOH . 
E 5 HOH A 29 629 54 HOH HOH . 
E 5 HOH A 30 630 50 HOH HOH . 
E 5 HOH A 31 631 46 HOH HOH . 
E 5 HOH A 32 632 51 HOH HOH . 
E 5 HOH A 33 633 52 HOH HOH . 
E 5 HOH A 34 634 24 HOH HOH . 
E 5 HOH A 35 635 2 HOH HOH . 
E 5 HOH A 36 636 3 HOH HOH . 
E 5 HOH A 37 637 17 HOH HOH . 
E 5 HOH A 38 638 45 HOH HOH . 
E 5 HOH A 39 639 15 HOH HOH . 
E 5 HOH A 40 640 22 HOH HOH . 
E 5 HOH A 41 641 31 HOH HOH . 
E 5 HOH A 42 642 30 HOH HOH . 
E 5 HOH A 43 643 37 HOH HOH . 
E 5 HOH A 44 644 40 HOH HOH . 
E 5 HOH A 45 645 56 HOH HOH . 
E 5 HOH A 46 646 10 HOH HOH . 
E 5 HOH A 47 647 39 HOH HOH . 
E 5 HOH A 48 648 20 HOH HOH . 
E 5 HOH A 49 649 53 HOH HOH . 
E 5 HOH A 50 650 32 HOH HOH . 
E 5 HOH A 51 651 33 HOH HOH . 
E 5 HOH A 52 652 48 HOH HOH . 
E 5 HOH A 53 653 38 HOH HOH . 
E 5 HOH A 54 654 11 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 O OAM 9YX . . . D 4 -23.129 -20.743 -9.071 1 63.17 ? OAM 9YX 503 A 1 
HETATM 2 P PAL 9YX . . . D 4 -22.646 -19.506 -9.764 1 65.08 ? PAL 9YX 503 A 1 
HETATM 3 O OAO 9YX . . . D 4 -21.586 -18.896 -8.647 1 59.79 ? OAO 9YX 503 A 1 
HETATM 4 O OAN 9YX . . . D 4 -23.79 -18.62 -10.006 1 64.78 ? OAN 9YX 503 A 1 
HETATM 5 O OAK 9YX . . . D 4 -21.748 -19.877 -10.993 1 72.19 ? OAK 9YX 503 A 1 
HETATM 6 C CAJ 9YX . . . D 4 -21.376 -18.595 -11.631 1 83.38 ? CAJ 9YX 503 A 1 
HETATM 7 C CAA 9YX . . . D 4 -20.877 -18.748 -12.942 1 86.52 ? CAA 9YX 503 A 1 
HETATM 8 C CAB 9YX . . . D 4 -19.489 -18.747 -13.092 1 95.84 ? CAB 9YX 503 A 1 
HETATM 9 N NAC 9YX . . . D 4 -18.832 -18.904 -14.326 1 87.26 ? NAC 9YX 503 A 1 
HETATM 10 C CAD 9YX . . . D 4 -19.563 -19.058 -15.423 1 92.15 ? CAD 9YX 503 A 1 
HETATM 11 C CAG 9YX . . . D 4 -18.893 -19.205 -16.636 1 81.47 ? CAG 9YX 503 A 1 
HETATM 12 C CAE 9YX . . . D 4 -20.959 -19.065 -15.313 1 92.85 ? CAE 9YX 503 A 1 
HETATM 13 O OAH 9YX . . . D 4 -21.669 -19.241 -16.448 1 90.86 ? OAH 9YX 503 A 1 
HETATM 14 C CAF 9YX . . . D 4 -21.648 -18.921 -14.104 1 96.81 ? CAF 9YX 503 A 1 
HETATM 15 C CAI 9YX . . . D 4 -23.067 -18.879 -14.074 1 117.65 ? CAI 9YX 503 A 1 
HETATM 16 N N 9YX . . . D 4 -23.551 -18.474 -15.414 1 124.15 ? N 9YX 503 A 1 
HETATM 17 S SAS 9YX . . . D 4 -24.259 -20.177 -13.88 1 133.46 ? SAS 9YX 503 A 1 
HETATM 18 C CB 9YX . . . D 4 -25.632 -19.121 -14.282 1 112.72 ? CB 9YX 503 A 1 
HETATM 19 C CA 9YX . . . D 4 -24.945 -18.069 -15.182 1 110.15 ? CA 9YX 503 A 1 
HETATM 20 C C 9YX . . . D 4 -25.76 -17.826 -16.46 1 102.73 ? C 9YX 503 A 1 
HETATM 21 O OXT 9YX . . . D 4 -25.308 -18.178 -17.575 1 90.32 ? OXT 9YX 503 A 1 
HETATM 22 O O 9YX . . . D 4 -26.814 -17.201 -16.282 1 112.79 ? O 9YX 503 A 1 
#
_model_server_stats.io_time_ms              28 
_model_server_stats.parse_time_ms           25 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           212 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           22 
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