data_5KR6
#
_model_server_result.job_id            veLIiFNbExp28ljHdxb0ag 
_model_server_result.datetime_utc      '2025-07-31 01:07:07' 
_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          5kr6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":501}' 
#
_entry.id    5KR6 
#
_exptl.entry_id    5KR6 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              247.142 
_entity.id                          2 
_entity.src_method                  man 
_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                     2.6.1.18 
#
_cell.angle_alpha         90 
_cell.angle_beta          117.61 
_cell.angle_gamma         90 
_cell.entry_id            5KR6 
_cell.length_a            61.088 
_cell.length_b            123.24 
_cell.length_c            63.251 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5KR6 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 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 
#
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 308 A LYS 288 1_555 C C4A PLP . A PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.308 ? 
covale ? covale2 B NZ LYS 308 B LYS 288 1_555 D C4A PLP . B PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.373 ? 
#
_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                     5KR6 
_atom_sites.fract_transf_matrix[1][1]    0.01637 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.00856 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008114 
_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]    0.017841 
_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 1 501 470 PLP PLP . 
D 2 PLP B 1 501 470 PLP PLP . 
E 3 HOH A 1 601 111 HOH HOH . 
E 3 HOH A 2 602 95 HOH HOH . 
E 3 HOH A 3 603 198 HOH HOH . 
E 3 HOH A 4 604 194 HOH HOH . 
E 3 HOH A 5 605 181 HOH HOH . 
E 3 HOH A 6 606 97 HOH HOH . 
E 3 HOH A 7 607 90 HOH HOH . 
E 3 HOH A 8 608 169 HOH HOH . 
E 3 HOH A 9 609 101 HOH HOH . 
E 3 HOH A 10 610 89 HOH HOH . 
E 3 HOH A 11 611 55 HOH HOH . 
E 3 HOH A 12 612 207 HOH HOH . 
E 3 HOH A 13 613 10 HOH HOH . 
E 3 HOH A 14 614 104 HOH HOH . 
E 3 HOH A 15 615 31 HOH HOH . 
E 3 HOH A 16 616 61 HOH HOH . 
E 3 HOH A 17 617 99 HOH HOH . 
E 3 HOH A 18 618 103 HOH HOH . 
E 3 HOH A 19 619 6 HOH HOH . 
E 3 HOH A 20 620 128 HOH HOH . 
E 3 HOH A 21 621 105 HOH HOH . 
E 3 HOH A 22 622 24 HOH HOH . 
E 3 HOH A 23 623 22 HOH HOH . 
E 3 HOH A 24 624 52 HOH HOH . 
E 3 HOH A 25 625 17 HOH HOH . 
E 3 HOH A 26 626 33 HOH HOH . 
E 3 HOH A 27 627 96 HOH HOH . 
E 3 HOH A 28 628 98 HOH HOH . 
E 3 HOH A 29 629 76 HOH HOH . 
E 3 HOH A 30 630 158 HOH HOH . 
E 3 HOH A 31 631 8 HOH HOH . 
E 3 HOH A 32 632 4 HOH HOH . 
E 3 HOH A 33 633 166 HOH HOH . 
E 3 HOH A 34 634 1 HOH HOH . 
E 3 HOH A 35 635 42 HOH HOH . 
E 3 HOH A 36 636 40 HOH HOH . 
E 3 HOH A 37 637 2 HOH HOH . 
E 3 HOH A 38 638 35 HOH HOH . 
E 3 HOH A 39 639 14 HOH HOH . 
E 3 HOH A 40 640 11 HOH HOH . 
E 3 HOH A 41 641 146 HOH HOH . 
E 3 HOH A 42 642 32 HOH HOH . 
E 3 HOH A 43 643 122 HOH HOH . 
E 3 HOH A 44 644 27 HOH HOH . 
E 3 HOH A 45 645 161 HOH HOH . 
E 3 HOH A 46 646 137 HOH HOH . 
E 3 HOH A 47 647 23 HOH HOH . 
E 3 HOH A 48 648 159 HOH HOH . 
E 3 HOH A 49 649 133 HOH HOH . 
E 3 HOH A 50 650 18 HOH HOH . 
E 3 HOH A 51 651 9 HOH HOH . 
E 3 HOH A 52 652 39 HOH HOH . 
E 3 HOH A 53 653 197 HOH HOH . 
E 3 HOH A 54 654 84 HOH HOH . 
E 3 HOH A 55 655 30 HOH HOH . 
E 3 HOH A 56 656 175 HOH HOH . 
E 3 HOH A 57 657 109 HOH HOH . 
E 3 HOH A 58 658 62 HOH HOH . 
E 3 HOH A 59 659 85 HOH HOH . 
E 3 HOH A 60 660 56 HOH HOH . 
E 3 HOH A 61 661 12 HOH HOH . 
E 3 HOH A 62 662 36 HOH HOH . 
E 3 HOH A 63 663 38 HOH HOH . 
E 3 HOH A 64 664 83 HOH HOH . 
E 3 HOH A 65 665 78 HOH HOH . 
E 3 HOH A 66 666 65 HOH HOH . 
E 3 HOH A 67 667 20 HOH HOH . 
E 3 HOH A 68 668 41 HOH HOH . 
E 3 HOH A 69 669 34 HOH HOH . 
E 3 HOH A 70 670 16 HOH HOH . 
E 3 HOH A 71 671 173 HOH HOH . 
E 3 HOH A 72 672 183 HOH HOH . 
E 3 HOH A 73 673 25 HOH HOH . 
E 3 HOH A 74 674 26 HOH HOH . 
E 3 HOH A 75 675 196 HOH HOH . 
E 3 HOH A 76 676 94 HOH HOH . 
E 3 HOH A 77 677 7 HOH HOH . 
E 3 HOH A 78 678 184 HOH HOH . 
E 3 HOH A 79 679 73 HOH HOH . 
E 3 HOH A 80 680 208 HOH HOH . 
E 3 HOH A 81 681 87 HOH HOH . 
E 3 HOH A 82 682 200 HOH HOH . 
E 3 HOH A 83 683 134 HOH HOH . 
E 3 HOH A 84 684 58 HOH HOH . 
E 3 HOH A 85 685 108 HOH HOH . 
E 3 HOH A 86 686 185 HOH HOH . 
E 3 HOH A 87 687 19 HOH HOH . 
E 3 HOH A 88 688 93 HOH HOH . 
E 3 HOH A 89 689 138 HOH HOH . 
E 3 HOH A 90 690 202 HOH HOH . 
E 3 HOH A 91 691 13 HOH HOH . 
E 3 HOH A 92 692 177 HOH HOH . 
E 3 HOH A 93 693 102 HOH HOH . 
E 3 HOH A 94 694 67 HOH HOH . 
E 3 HOH A 95 695 28 HOH HOH . 
E 3 HOH A 96 696 168 HOH HOH . 
E 3 HOH A 97 697 44 HOH HOH . 
E 3 HOH A 98 698 43 HOH HOH . 
E 3 HOH A 99 699 15 HOH HOH . 
E 3 HOH A 100 700 45 HOH HOH . 
E 3 HOH A 101 701 203 HOH HOH . 
E 3 HOH A 102 702 130 HOH HOH . 
E 3 HOH A 103 703 132 HOH HOH . 
E 3 HOH A 104 704 29 HOH HOH . 
E 3 HOH A 105 705 215 HOH HOH . 
E 3 HOH A 106 706 139 HOH HOH . 
E 3 HOH A 107 707 201 HOH HOH . 
E 3 HOH A 108 708 136 HOH HOH . 
E 3 HOH A 109 709 187 HOH HOH . 
E 3 HOH A 110 710 127 HOH HOH . 
E 3 HOH A 111 711 167 HOH HOH . 
F 3 HOH B 1 601 119 HOH HOH . 
F 3 HOH B 2 602 150 HOH HOH . 
F 3 HOH B 3 603 217 HOH HOH . 
F 3 HOH B 4 604 216 HOH HOH . 
F 3 HOH B 5 605 178 HOH HOH . 
F 3 HOH B 6 606 123 HOH HOH . 
F 3 HOH B 7 607 145 HOH HOH . 
F 3 HOH B 8 608 135 HOH HOH . 
F 3 HOH B 9 609 86 HOH HOH . 
F 3 HOH B 10 610 179 HOH HOH . 
F 3 HOH B 11 611 141 HOH HOH . 
F 3 HOH B 12 612 162 HOH HOH . 
F 3 HOH B 13 613 212 HOH HOH . 
F 3 HOH B 14 614 115 HOH HOH . 
F 3 HOH B 15 615 142 HOH HOH . 
F 3 HOH B 16 616 53 HOH HOH . 
F 3 HOH B 17 617 147 HOH HOH . 
F 3 HOH B 18 618 77 HOH HOH . 
F 3 HOH B 19 619 164 HOH HOH . 
F 3 HOH B 20 620 154 HOH HOH . 
F 3 HOH B 21 621 118 HOH HOH . 
F 3 HOH B 22 622 205 HOH HOH . 
F 3 HOH B 23 623 125 HOH HOH . 
F 3 HOH B 24 624 74 HOH HOH . 
F 3 HOH B 25 625 165 HOH HOH . 
F 3 HOH B 26 626 144 HOH HOH . 
F 3 HOH B 27 627 3 HOH HOH . 
F 3 HOH B 28 628 148 HOH HOH . 
F 3 HOH B 29 629 176 HOH HOH . 
F 3 HOH B 30 630 188 HOH HOH . 
F 3 HOH B 31 631 100 HOH HOH . 
F 3 HOH B 32 632 214 HOH HOH . 
F 3 HOH B 33 633 107 HOH HOH . 
F 3 HOH B 34 634 54 HOH HOH . 
F 3 HOH B 35 635 47 HOH HOH . 
F 3 HOH B 36 636 59 HOH HOH . 
F 3 HOH B 37 637 110 HOH HOH . 
F 3 HOH B 38 638 80 HOH HOH . 
F 3 HOH B 39 639 5 HOH HOH . 
F 3 HOH B 40 640 75 HOH HOH . 
F 3 HOH B 41 641 64 HOH HOH . 
F 3 HOH B 42 642 180 HOH HOH . 
F 3 HOH B 43 643 106 HOH HOH . 
F 3 HOH B 44 644 121 HOH HOH . 
F 3 HOH B 45 645 51 HOH HOH . 
F 3 HOH B 46 646 69 HOH HOH . 
F 3 HOH B 47 647 37 HOH HOH . 
F 3 HOH B 48 648 92 HOH HOH . 
F 3 HOH B 49 649 82 HOH HOH . 
F 3 HOH B 50 650 163 HOH HOH . 
F 3 HOH B 51 651 153 HOH HOH . 
F 3 HOH B 52 652 191 HOH HOH . 
F 3 HOH B 53 653 113 HOH HOH . 
F 3 HOH B 54 654 70 HOH HOH . 
F 3 HOH B 55 655 88 HOH HOH . 
F 3 HOH B 56 656 117 HOH HOH . 
F 3 HOH B 57 657 170 HOH HOH . 
F 3 HOH B 58 658 57 HOH HOH . 
F 3 HOH B 59 659 49 HOH HOH . 
F 3 HOH B 60 660 50 HOH HOH . 
F 3 HOH B 61 661 72 HOH HOH . 
F 3 HOH B 62 662 209 HOH HOH . 
F 3 HOH B 63 663 192 HOH HOH . 
F 3 HOH B 64 664 182 HOH HOH . 
F 3 HOH B 65 665 91 HOH HOH . 
F 3 HOH B 66 666 193 HOH HOH . 
F 3 HOH B 67 667 63 HOH HOH . 
F 3 HOH B 68 668 171 HOH HOH . 
F 3 HOH B 69 669 151 HOH HOH . 
F 3 HOH B 70 670 218 HOH HOH . 
F 3 HOH B 71 671 116 HOH HOH . 
F 3 HOH B 72 672 71 HOH HOH . 
F 3 HOH B 73 673 160 HOH HOH . 
F 3 HOH B 74 674 79 HOH HOH . 
F 3 HOH B 75 675 68 HOH HOH . 
F 3 HOH B 76 676 60 HOH HOH . 
F 3 HOH B 77 677 195 HOH HOH . 
F 3 HOH B 78 678 190 HOH HOH . 
F 3 HOH B 79 679 213 HOH HOH . 
F 3 HOH B 80 680 129 HOH HOH . 
F 3 HOH B 81 681 186 HOH HOH . 
F 3 HOH B 82 682 155 HOH HOH . 
F 3 HOH B 83 683 48 HOH HOH . 
F 3 HOH B 84 684 66 HOH HOH . 
F 3 HOH B 85 685 156 HOH HOH . 
F 3 HOH B 86 686 149 HOH HOH . 
F 3 HOH B 87 687 210 HOH HOH . 
F 3 HOH B 88 688 199 HOH HOH . 
F 3 HOH B 89 689 46 HOH HOH . 
F 3 HOH B 90 690 174 HOH HOH . 
F 3 HOH B 91 691 143 HOH HOH . 
F 3 HOH B 92 692 81 HOH HOH . 
F 3 HOH B 93 693 112 HOH HOH . 
F 3 HOH B 94 694 21 HOH HOH . 
F 3 HOH B 95 695 131 HOH HOH . 
F 3 HOH B 96 696 120 HOH HOH . 
F 3 HOH B 97 697 157 HOH HOH . 
F 3 HOH B 98 698 189 HOH HOH . 
F 3 HOH B 99 699 124 HOH HOH . 
F 3 HOH B 100 700 204 HOH HOH . 
F 3 HOH B 101 701 126 HOH HOH . 
F 3 HOH B 102 702 172 HOH HOH . 
F 3 HOH B 103 703 206 HOH HOH . 
F 3 HOH B 104 704 152 HOH HOH . 
F 3 HOH B 105 705 211 HOH HOH . 
F 3 HOH B 106 706 114 HOH HOH . 
F 3 HOH B 107 707 140 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 . . . D 2 92.705 -20.486 13.962 1 19.16 ? N1 PLP 501 B 1 
HETATM 2 C C2 PLP . . . D 2 93.944 -20.975 14.148 1 19.93 ? C2 PLP 501 B 1 
HETATM 3 C C2A PLP . . . D 2 94.255 -22.441 13.952 1 20.3 ? C2A PLP 501 B 1 
HETATM 4 C C3 PLP . . . D 2 95.06 -20.06 14.488 1 22.27 ? C3 PLP 501 B 1 
HETATM 5 O O3 PLP . . . D 2 96.346 -20.555 14.627 1 23.81 ? O3 PLP 501 B 1 
HETATM 6 C C4 PLP . . . D 2 94.784 -18.605 14.657 1 22.2 ? C4 PLP 501 B 1 
HETATM 7 C C4A PLP . . . D 2 95.973 -17.671 14.929 1 23.93 ? C4A PLP 501 B 1 
HETATM 8 C C5 PLP . . . D 2 93.327 -18.218 14.468 1 20.27 ? C5 PLP 501 B 1 
HETATM 9 C C6 PLP . . . D 2 92.374 -19.186 14.139 1 18.96 ? C6 PLP 501 B 1 
HETATM 10 C C5A PLP . . . D 2 92.931 -16.766 14.619 1 19.96 ? C5A PLP 501 B 1 
HETATM 11 O O4P PLP . . . D 2 93.641 -15.928 13.706 1 17.63 ? O4P PLP 501 B 1 
HETATM 12 P P PLP . . . D 2 93.799 -14.325 14.049 1 20.31 ? P PLP 501 B 1 
HETATM 13 O O1P PLP . . . D 2 94.281 -13.844 12.689 1 18.66 ? O1P PLP 501 B 1 
HETATM 14 O O2P PLP . . . D 2 92.439 -13.887 14.393 1 17.75 ? O2P PLP 501 B 1 
HETATM 15 O O3P PLP . . . D 2 94.745 -14.264 15.203 1 19 ? O3P PLP 501 B 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    20 
_model_server_stats.query_time_ms           257 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           15 
#