data_1ORD
#
_model_server_result.job_id            oSViRFGqGjgHkl_mElZUQQ 
_model_server_result.datetime_utc      '2024-10-11 14:25:38' 
_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          1ord 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":731}' 
#
_entry.id    1ORD 
#
_exptl.entry_id    1ORD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              247.142 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "PYRIDOXAL-5'-PHOSPHATE" 
_entity.pdbx_number_of_molecules    2 
_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            1ORD 
_cell.length_a            195.6 
_cell.length_b            195.6 
_cell.length_c            97.6 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1ORD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        168 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 6' 
#
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 dimeric 2 author_and_software_defined_assembly 1 
PISA dodecameric 12 software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F 1 1 
A,B,C,D,E,F 2 1,2,3,4,5,6 
#
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' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 
3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 
4 'crystal symmetry operation' 4_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 
5 'crystal symmetry operation' 5_555 y,-x+y,z 0.5 0.866025 0 -0.866025 0.5 0 0 0 1 0 0 0 
6 'crystal symmetry operation' 6_555 x-y,x,z 0.5 -0.866025 0 0.866025 0.5 0 0 0 1 0 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 D 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 A NZ LYS 355 A LYS 355 1_555 C C4A PLP . A PLP 731 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.363 ? 
covale ? covale2 B NZ LYS 355 B LYS 355 1_555 D C4A PLP . B PLP 731 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.343 ? 
#
_chem_comp.formula           'C8 H10 N O6 P' 
_chem_comp.formula_weight    247.142 
_chem_comp.id                PLP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "PYRIDOXAL-5'-PHOSPHATE" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'VITAMIN B6 Phosphate' 
#
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
N1 C2 PLP doub 260 n y 
N1 C6 PLP sing 261 n y 
C2 C2A PLP sing 262 n n 
C2 C3 PLP sing 263 n y 
C2A H2A1 PLP sing 264 n n 
C2A H2A2 PLP sing 265 n n 
C2A H2A3 PLP sing 266 n n 
C3 O3 PLP sing 267 n n 
C3 C4 PLP doub 268 n y 
O3 HO3 PLP sing 269 n n 
C4 C4A PLP sing 270 n n 
C4 C5 PLP sing 271 n y 
C4A O4A PLP doub 272 n n 
C4A H4A PLP sing 273 n n 
C5 C6 PLP doub 274 n y 
C5 C5A PLP sing 275 n n 
C6 H6 PLP sing 276 n n 
C5A O4P PLP sing 277 n n 
C5A H5A1 PLP sing 278 n n 
C5A H5A2 PLP sing 279 n n 
O4P P PLP sing 280 n n 
P O1P PLP doub 281 n n 
P O2P PLP sing 282 n n 
P O3P PLP sing 283 n n 
O2P HOP2 PLP sing 284 n n 
O3P HOP3 PLP sing 285 n n 
#
_atom_sites.entry_id                     1ORD 
_atom_sites.fract_transf_matrix[1][1]    0.005112 
_atom_sites.fract_transf_matrix[1][2]    0.002952 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.005903 
_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]    0.010246 
_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 PLP A 1 731 355 PLP PLP . 
D 2 PLP B 1 731 355 PLP PLP . 
E 3 HOH A 1 732 1 HOH HOH . 
E 3 HOH A 2 733 2 HOH HOH . 
E 3 HOH A 3 734 3 HOH HOH . 
E 3 HOH A 4 735 4 HOH HOH . 
E 3 HOH A 5 736 5 HOH HOH . 
E 3 HOH A 6 737 6 HOH HOH . 
E 3 HOH A 7 738 8 HOH HOH . 
E 3 HOH A 8 739 9 HOH HOH . 
E 3 HOH A 9 740 12 HOH HOH . 
E 3 HOH A 10 741 13 HOH HOH . 
E 3 HOH A 11 742 14 HOH HOH . 
E 3 HOH A 12 743 15 HOH HOH . 
E 3 HOH A 13 744 16 HOH HOH . 
E 3 HOH A 14 745 17 HOH HOH . 
E 3 HOH A 15 746 18 HOH HOH . 
E 3 HOH A 16 747 19 HOH HOH . 
E 3 HOH A 17 748 20 HOH HOH . 
E 3 HOH A 18 749 21 HOH HOH . 
E 3 HOH A 19 750 22 HOH HOH . 
E 3 HOH A 20 751 23 HOH HOH . 
E 3 HOH A 21 752 24 HOH HOH . 
E 3 HOH A 22 753 25 HOH HOH . 
E 3 HOH A 23 754 26 HOH HOH . 
E 3 HOH A 24 755 27 HOH HOH . 
E 3 HOH A 25 756 28 HOH HOH . 
E 3 HOH A 26 757 29 HOH HOH . 
E 3 HOH A 27 758 30 HOH HOH . 
E 3 HOH A 28 759 31 HOH HOH . 
E 3 HOH A 29 760 32 HOH HOH . 
E 3 HOH A 30 761 33 HOH HOH . 
E 3 HOH A 31 762 34 HOH HOH . 
E 3 HOH A 32 763 35 HOH HOH . 
E 3 HOH A 33 764 36 HOH HOH . 
E 3 HOH A 34 765 38 HOH HOH . 
E 3 HOH A 35 766 39 HOH HOH . 
E 3 HOH A 36 767 54 HOH HOH . 
E 3 HOH A 37 768 71 HOH HOH . 
E 3 HOH A 38 769 86 HOH HOH . 
E 3 HOH A 39 770 89 HOH HOH . 
E 3 HOH A 40 771 98 HOH HOH . 
E 3 HOH A 41 772 100 HOH HOH . 
E 3 HOH A 42 773 101 HOH HOH . 
E 3 HOH A 43 774 102 HOH HOH . 
E 3 HOH A 44 775 103 HOH HOH . 
E 3 HOH A 45 776 105 HOH HOH . 
E 3 HOH A 46 777 106 HOH HOH . 
E 3 HOH A 47 778 107 HOH HOH . 
F 3 HOH B 1 732 7 HOH HOH . 
F 3 HOH B 2 733 10 HOH HOH . 
F 3 HOH B 3 734 11 HOH HOH . 
F 3 HOH B 4 735 37 HOH HOH . 
F 3 HOH B 5 736 40 HOH HOH . 
F 3 HOH B 6 737 41 HOH HOH . 
F 3 HOH B 7 738 42 HOH HOH . 
F 3 HOH B 8 739 43 HOH HOH . 
F 3 HOH B 9 740 44 HOH HOH . 
F 3 HOH B 10 741 45 HOH HOH . 
F 3 HOH B 11 742 46 HOH HOH . 
F 3 HOH B 12 743 47 HOH HOH . 
F 3 HOH B 13 744 48 HOH HOH . 
F 3 HOH B 14 745 49 HOH HOH . 
F 3 HOH B 15 746 50 HOH HOH . 
F 3 HOH B 16 747 51 HOH HOH . 
F 3 HOH B 17 748 52 HOH HOH . 
F 3 HOH B 18 749 53 HOH HOH . 
F 3 HOH B 19 750 55 HOH HOH . 
F 3 HOH B 20 751 56 HOH HOH . 
F 3 HOH B 21 752 57 HOH HOH . 
F 3 HOH B 22 753 58 HOH HOH . 
F 3 HOH B 23 754 59 HOH HOH . 
F 3 HOH B 24 755 60 HOH HOH . 
F 3 HOH B 25 756 61 HOH HOH . 
F 3 HOH B 26 757 62 HOH HOH . 
F 3 HOH B 27 758 63 HOH HOH . 
F 3 HOH B 28 759 64 HOH HOH . 
F 3 HOH B 29 760 65 HOH HOH . 
F 3 HOH B 30 761 66 HOH HOH . 
F 3 HOH B 31 762 67 HOH HOH . 
F 3 HOH B 32 763 68 HOH HOH . 
F 3 HOH B 33 764 69 HOH HOH . 
F 3 HOH B 34 765 70 HOH HOH . 
F 3 HOH B 35 766 72 HOH HOH . 
F 3 HOH B 36 767 73 HOH HOH . 
F 3 HOH B 37 768 74 HOH HOH . 
F 3 HOH B 38 769 75 HOH HOH . 
F 3 HOH B 39 770 76 HOH HOH . 
F 3 HOH B 40 771 77 HOH HOH . 
F 3 HOH B 41 772 78 HOH HOH . 
F 3 HOH B 42 773 79 HOH HOH . 
F 3 HOH B 43 774 80 HOH HOH . 
F 3 HOH B 44 775 81 HOH HOH . 
F 3 HOH B 45 776 82 HOH HOH . 
F 3 HOH B 46 777 83 HOH HOH . 
F 3 HOH B 47 778 84 HOH HOH . 
F 3 HOH B 48 779 85 HOH HOH . 
F 3 HOH B 49 780 87 HOH HOH . 
F 3 HOH B 50 781 88 HOH HOH . 
F 3 HOH B 51 782 90 HOH HOH . 
F 3 HOH B 52 783 91 HOH HOH . 
F 3 HOH B 53 784 92 HOH HOH . 
F 3 HOH B 54 785 93 HOH HOH . 
F 3 HOH B 55 786 94 HOH HOH . 
F 3 HOH B 56 787 95 HOH HOH . 
F 3 HOH B 57 788 96 HOH HOH . 
F 3 HOH B 58 789 97 HOH HOH . 
F 3 HOH B 59 790 99 HOH HOH . 
F 3 HOH B 60 791 104 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 PLP . . . C 2 68.541 25.635 35.163 1 15.25 ? N1 PLP 731 A 1 
HETATM 2 C C2 PLP . . . C 2 67.61 25.903 34.15 1 15.25 ? C2 PLP 731 A 1 
HETATM 3 C C2A PLP . . . C 2 68.018 25.94 32.626 1 15.25 ? C2A PLP 731 A 1 
HETATM 4 C C3 PLP . . . C 2 66.279 26.208 34.477 1 15.25 ? C3 PLP 731 A 1 
HETATM 5 O O3 PLP . . . C 2 65.353 26.501 33.462 1 15.25 ? O3 PLP 731 A 1 
HETATM 6 C C4 PLP . . . C 2 65.875 26.229 35.811 1 15.25 ? C4 PLP 731 A 1 
HETATM 7 C C4A PLP . . . C 2 64.374 26.123 36.161 1 15.25 ? C4A PLP 731 A 1 
HETATM 8 C C5 PLP . . . C 2 66.806 26.006 36.804 1 15.25 ? C5 PLP 731 A 1 
HETATM 9 C C6 PLP . . . C 2 68.137 25.698 36.478 1 15.25 ? C6 PLP 731 A 1 
HETATM 10 C C5A PLP . . . C 2 66.336 26.181 38.261 1 15.25 ? C5A PLP 731 A 1 
HETATM 11 O O4P PLP . . . C 2 65.79 24.992 38.784 1 15.25 ? O4P PLP 731 A 1 
HETATM 12 P P PLP . . . C 2 64.338 24.742 39.499 1 15.25 ? P PLP 731 A 1 
HETATM 13 O O1P PLP . . . C 2 64.029 23.382 38.966 1 15.25 ? O1P PLP 731 A 1 
HETATM 14 O O2P PLP . . . C 2 63.322 25.592 38.881 1 15.25 ? O2P PLP 731 A 1 
HETATM 15 O O3P PLP . . . C 2 64.325 24.845 40.987 1 15.25 ? O3P PLP 731 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           293 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           15 
#