data_6KFU
#
_model_server_result.job_id            X5g3PtNYpYk-O17-RNvGqA 
_model_server_result.datetime_utc      '2024-12-27 04:47:54' 
_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          6kfu 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":601}' 
#
_entry.id    6KFU 
#
_exptl.entry_id    6KFU 
_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    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            6KFU 
_cell.length_a            73.939 
_cell.length_b            73.939 
_cell.length_c            209.617 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6KFU 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        151 
_symmetry.space_group_name_Hall    'P 31 2 (x,y,z+1/3)' 
_symmetry.space_group_name_H-M     'P 31 1 2' 
#
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
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' 5_556 -x+y,y,-z+4/3 -1 0 0 0 1 0 0 0 -1 0 0 279.489333 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_struct_conn.conn_type_id                   covale 
_struct_conn.details                        ? 
_struct_conn.id                             covale1 
_struct_conn.ptnr1_label_asym_id            A 
_struct_conn.ptnr1_label_atom_id            NZ 
_struct_conn.ptnr1_label_comp_id            LYS 
_struct_conn.ptnr1_label_seq_id             381 
_struct_conn.ptnr1_auth_asym_id             A 
_struct_conn.ptnr1_auth_comp_id             LYS 
_struct_conn.ptnr1_auth_seq_id              381 
_struct_conn.ptnr1_symmetry                 1_555 
_struct_conn.ptnr2_label_asym_id            B 
_struct_conn.ptnr2_label_atom_id            C4A 
_struct_conn.ptnr2_label_comp_id            PLP 
_struct_conn.ptnr2_label_seq_id             . 
_struct_conn.ptnr2_auth_asym_id             A 
_struct_conn.ptnr2_auth_comp_id             PLP 
_struct_conn.ptnr2_auth_seq_id              601 
_struct_conn.ptnr2_symmetry                 1_555 
_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                1.474 
_struct_conn.pdbx_value_order               ? 
#
_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 273 n y 
N1 C6 PLP sing 274 n y 
C2 C2A PLP sing 275 n n 
C2 C3 PLP sing 276 n y 
C2A H2A1 PLP sing 277 n n 
C2A H2A2 PLP sing 278 n n 
C2A H2A3 PLP sing 279 n n 
C3 O3 PLP sing 280 n n 
C3 C4 PLP doub 281 n y 
O3 HO3 PLP sing 282 n n 
C4 C4A PLP sing 283 n n 
C4 C5 PLP sing 284 n y 
C4A O4A PLP doub 285 n n 
C4A H4A PLP sing 286 n n 
C5 C6 PLP doub 287 n y 
C5 C5A PLP sing 288 n n 
C6 H6 PLP sing 289 n n 
C5A O4P PLP sing 290 n n 
C5A H5A1 PLP sing 291 n n 
C5A H5A2 PLP sing 292 n n 
O4P P PLP sing 293 n n 
P O1P PLP doub 294 n n 
P O2P PLP sing 295 n n 
P O3P PLP sing 296 n n 
O2P HOP2 PLP sing 297 n n 
O3P HOP3 PLP sing 298 n n 
#
_atom_sites.entry_id                     6KFU 
_atom_sites.fract_transf_matrix[1][1]    0.013525 
_atom_sites.fract_transf_matrix[1][2]    0.007808 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.015617 
_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]    0.004771 
_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 PLP A 1 601 551 PLP PLP . 
C 3 GOL A 1 602 552 GOL GOL . 
D 4 HOH A 1 701 18 HOH HOH . 
D 4 HOH A 2 702 6 HOH HOH . 
D 4 HOH A 3 703 55 HOH HOH . 
D 4 HOH A 4 704 47 HOH HOH . 
D 4 HOH A 5 705 17 HOH HOH . 
D 4 HOH A 6 706 1 HOH HOH . 
D 4 HOH A 7 707 72 HOH HOH . 
D 4 HOH A 8 708 13 HOH HOH . 
D 4 HOH A 9 709 92 HOH HOH . 
D 4 HOH A 10 710 44 HOH HOH . 
D 4 HOH A 11 711 9 HOH HOH . 
D 4 HOH A 12 712 42 HOH HOH . 
D 4 HOH A 13 713 25 HOH HOH . 
D 4 HOH A 14 714 93 HOH HOH . 
D 4 HOH A 15 715 4 HOH HOH . 
D 4 HOH A 16 716 12 HOH HOH . 
D 4 HOH A 17 717 57 HOH HOH . 
D 4 HOH A 18 718 81 HOH HOH . 
D 4 HOH A 19 719 7 HOH HOH . 
D 4 HOH A 20 720 8 HOH HOH . 
D 4 HOH A 21 721 102 HOH HOH . 
D 4 HOH A 22 722 40 HOH HOH . 
D 4 HOH A 23 723 31 HOH HOH . 
D 4 HOH A 24 724 20 HOH HOH . 
D 4 HOH A 25 725 11 HOH HOH . 
D 4 HOH A 26 726 10 HOH HOH . 
D 4 HOH A 27 727 35 HOH HOH . 
D 4 HOH A 28 728 54 HOH HOH . 
D 4 HOH A 29 729 107 HOH HOH . 
D 4 HOH A 30 730 62 HOH HOH . 
D 4 HOH A 31 731 5 HOH HOH . 
D 4 HOH A 32 732 49 HOH HOH . 
D 4 HOH A 33 733 41 HOH HOH . 
D 4 HOH A 34 734 22 HOH HOH . 
D 4 HOH A 35 735 51 HOH HOH . 
D 4 HOH A 36 736 91 HOH HOH . 
D 4 HOH A 37 737 27 HOH HOH . 
D 4 HOH A 38 738 33 HOH HOH . 
D 4 HOH A 39 739 37 HOH HOH . 
D 4 HOH A 40 740 100 HOH HOH . 
D 4 HOH A 41 741 80 HOH HOH . 
D 4 HOH A 42 742 75 HOH HOH . 
D 4 HOH A 43 743 56 HOH HOH . 
D 4 HOH A 44 744 3 HOH HOH . 
D 4 HOH A 45 745 98 HOH HOH . 
D 4 HOH A 46 746 59 HOH HOH . 
D 4 HOH A 47 747 30 HOH HOH . 
D 4 HOH A 48 748 48 HOH HOH . 
D 4 HOH A 49 749 26 HOH HOH . 
D 4 HOH A 50 750 21 HOH HOH . 
D 4 HOH A 51 751 43 HOH HOH . 
D 4 HOH A 52 752 63 HOH HOH . 
D 4 HOH A 53 753 2 HOH HOH . 
D 4 HOH A 54 754 16 HOH HOH . 
D 4 HOH A 55 755 60 HOH HOH . 
D 4 HOH A 56 756 19 HOH HOH . 
D 4 HOH A 57 757 109 HOH HOH . 
D 4 HOH A 58 758 89 HOH HOH . 
D 4 HOH A 59 759 83 HOH HOH . 
D 4 HOH A 60 760 23 HOH HOH . 
D 4 HOH A 61 761 14 HOH HOH . 
D 4 HOH A 62 762 46 HOH HOH . 
D 4 HOH A 63 763 39 HOH HOH . 
D 4 HOH A 64 764 38 HOH HOH . 
D 4 HOH A 65 765 112 HOH HOH . 
D 4 HOH A 66 766 97 HOH HOH . 
D 4 HOH A 67 767 82 HOH HOH . 
D 4 HOH A 68 768 61 HOH HOH . 
D 4 HOH A 69 769 66 HOH HOH . 
D 4 HOH A 70 770 34 HOH HOH . 
D 4 HOH A 71 771 108 HOH HOH . 
D 4 HOH A 72 772 96 HOH HOH . 
D 4 HOH A 73 773 52 HOH HOH . 
D 4 HOH A 74 774 29 HOH HOH . 
D 4 HOH A 75 775 24 HOH HOH . 
D 4 HOH A 76 776 113 HOH HOH . 
D 4 HOH A 77 777 110 HOH HOH . 
D 4 HOH A 78 778 36 HOH HOH . 
D 4 HOH A 79 779 115 HOH HOH . 
D 4 HOH A 80 780 95 HOH HOH . 
D 4 HOH A 81 781 50 HOH HOH . 
D 4 HOH A 82 782 65 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 . . . B 2 -1.791 23.674 127.849 1 37.78 ? N1 PLP 601 A 1 
HETATM 2 C C2 PLP . . . B 2 -1.587 24.347 126.69 1 35.08 ? C2 PLP 601 A 1 
HETATM 3 C C2A PLP . . . B 2 -2.338 23.947 125.448 1 36.55 ? C2A PLP 601 A 1 
HETATM 4 C C3 PLP . . . B 2 -0.627 25.478 126.644 1 34.42 ? C3 PLP 601 A 1 
HETATM 5 O O3 PLP . . . B 2 -0.405 26.171 125.492 1 43.06 ? O3 PLP 601 A 1 
HETATM 6 C C4 PLP . . . B 2 0.081 25.825 127.896 1 34.54 ? C4 PLP 601 A 1 
HETATM 7 C C4A PLP . . . B 2 1.057 26.937 127.95 1 38.64 ? C4A PLP 601 A 1 
HETATM 8 C C5 PLP . . . B 2 -0.231 25.011 129.095 1 37.09 ? C5 PLP 601 A 1 
HETATM 9 C C6 PLP . . . B 2 -1.157 23.975 128.996 1 34.33 ? C6 PLP 601 A 1 
HETATM 10 C C5A PLP . . . B 2 0.45 25.302 130.413 1 33.55 ? C5A PLP 601 A 1 
HETATM 11 O O4P PLP . . . B 2 0.183 26.649 130.798 1 42.44 ? O4P PLP 601 A 1 
HETATM 12 P P PLP . . . B 2 0.85 27.267 132.126 1 37.81 ? P PLP 601 A 1 
HETATM 13 O O1P PLP . . . B 2 2.305 27.435 131.759 1 27.68 ? O1P PLP 601 A 1 
HETATM 14 O O2P PLP . . . B 2 0.59 26.221 133.184 1 34.37 ? O2P PLP 601 A 1 
HETATM 15 O O3P PLP . . . B 2 0.107 28.565 132.338 1 34.6 ? O3P PLP 601 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           335 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           15 
#