data_8E9C
#
_model_server_result.job_id            4utdl0olCx6uQglPqRBDpg 
_model_server_result.datetime_utc      '2024-11-24 23:47:19' 
_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          8e9c 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":401}' 
#
_entry.id    8E9C 
#
_exptl.entry_id    8E9C 
_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            8E9C 
_cell.length_a            141.63 
_cell.length_b            141.63 
_cell.length_c            80.92 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8E9C 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        173 
_symmetry.space_group_name_Hall    'P 6c' 
_symmetry.space_group_name_H-M     'P 63' 
#
_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,G,H 
_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 F 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 256 A LYS 246 1_555 C C4A PLP . A PLP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.604 ? 
covale ? covale2 B NZ LYS 256 B LYS 246 1_555 F C4A PLP . B PLP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.639 ? 
#
_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                     8E9C 
_atom_sites.fract_transf_matrix[1][1]    0.007061 
_atom_sites.fract_transf_matrix[1][2]    0.004076 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008153 
_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]    0.012358 
_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 1 401 500 PLP PLP . 
D 3 SO4 A 1 402 600 SO4 SO4 . 
E 3 SO4 B 1 401 600 SO4 SO4 . 
F 2 PLP B 1 402 500 PLP PLP . 
G 4 HOH A 1 501 164 HOH HOH . 
G 4 HOH A 2 502 187 HOH HOH . 
G 4 HOH A 3 503 15 HOH HOH . 
G 4 HOH A 4 504 211 HOH HOH . 
G 4 HOH A 5 505 162 HOH HOH . 
G 4 HOH A 6 506 179 HOH HOH . 
G 4 HOH A 7 507 11 HOH HOH . 
G 4 HOH A 8 508 115 HOH HOH . 
G 4 HOH A 9 509 51 HOH HOH . 
G 4 HOH A 10 510 210 HOH HOH . 
G 4 HOH A 11 511 30 HOH HOH . 
G 4 HOH A 12 512 114 HOH HOH . 
G 4 HOH A 13 513 34 HOH HOH . 
G 4 HOH A 14 514 76 HOH HOH . 
G 4 HOH A 15 515 194 HOH HOH . 
G 4 HOH A 16 516 135 HOH HOH . 
G 4 HOH A 17 517 198 HOH HOH . 
G 4 HOH A 18 518 214 HOH HOH . 
G 4 HOH A 19 519 21 HOH HOH . 
G 4 HOH A 20 520 208 HOH HOH . 
G 4 HOH A 21 521 64 HOH HOH . 
G 4 HOH A 22 522 213 HOH HOH . 
G 4 HOH A 23 523 9 HOH HOH . 
G 4 HOH A 24 524 41 HOH HOH . 
G 4 HOH A 25 525 180 HOH HOH . 
G 4 HOH A 26 526 151 HOH HOH . 
G 4 HOH A 27 527 77 HOH HOH . 
G 4 HOH A 28 528 166 HOH HOH . 
G 4 HOH A 29 529 57 HOH HOH . 
G 4 HOH A 30 530 92 HOH HOH . 
G 4 HOH A 31 531 63 HOH HOH . 
G 4 HOH A 32 532 71 HOH HOH . 
G 4 HOH A 33 533 6 HOH HOH . 
G 4 HOH A 34 534 67 HOH HOH . 
G 4 HOH A 35 535 35 HOH HOH . 
G 4 HOH A 36 536 81 HOH HOH . 
G 4 HOH A 37 537 16 HOH HOH . 
G 4 HOH A 38 538 50 HOH HOH . 
G 4 HOH A 39 539 112 HOH HOH . 
G 4 HOH A 40 540 96 HOH HOH . 
G 4 HOH A 41 541 94 HOH HOH . 
G 4 HOH A 42 542 8 HOH HOH . 
G 4 HOH A 43 543 145 HOH HOH . 
G 4 HOH A 44 544 142 HOH HOH . 
G 4 HOH A 45 545 78 HOH HOH . 
G 4 HOH A 46 546 87 HOH HOH . 
G 4 HOH A 47 547 22 HOH HOH . 
G 4 HOH A 48 548 207 HOH HOH . 
G 4 HOH A 49 549 65 HOH HOH . 
G 4 HOH A 50 550 32 HOH HOH . 
G 4 HOH A 51 551 48 HOH HOH . 
G 4 HOH A 52 552 47 HOH HOH . 
G 4 HOH A 53 553 75 HOH HOH . 
G 4 HOH A 54 554 25 HOH HOH . 
G 4 HOH A 55 555 54 HOH HOH . 
G 4 HOH A 56 556 203 HOH HOH . 
G 4 HOH A 57 557 18 HOH HOH . 
G 4 HOH A 58 558 68 HOH HOH . 
G 4 HOH A 59 559 73 HOH HOH . 
G 4 HOH A 60 560 20 HOH HOH . 
G 4 HOH A 61 561 4 HOH HOH . 
G 4 HOH A 62 562 28 HOH HOH . 
G 4 HOH A 63 563 103 HOH HOH . 
G 4 HOH A 64 564 132 HOH HOH . 
G 4 HOH A 65 565 212 HOH HOH . 
G 4 HOH A 66 566 157 HOH HOH . 
G 4 HOH A 67 567 100 HOH HOH . 
G 4 HOH A 68 568 123 HOH HOH . 
G 4 HOH A 69 569 88 HOH HOH . 
G 4 HOH A 70 570 170 HOH HOH . 
G 4 HOH A 71 571 99 HOH HOH . 
G 4 HOH A 72 572 98 HOH HOH . 
G 4 HOH A 73 573 161 HOH HOH . 
G 4 HOH A 74 574 66 HOH HOH . 
G 4 HOH A 75 575 97 HOH HOH . 
G 4 HOH A 76 576 37 HOH HOH . 
G 4 HOH A 77 577 58 HOH HOH . 
G 4 HOH A 78 578 90 HOH HOH . 
G 4 HOH A 79 579 60 HOH HOH . 
G 4 HOH A 80 580 72 HOH HOH . 
G 4 HOH A 81 581 33 HOH HOH . 
G 4 HOH A 82 582 38 HOH HOH . 
G 4 HOH A 83 583 109 HOH HOH . 
G 4 HOH A 84 584 117 HOH HOH . 
G 4 HOH A 85 585 149 HOH HOH . 
G 4 HOH A 86 586 59 HOH HOH . 
G 4 HOH A 87 587 5 HOH HOH . 
G 4 HOH A 88 588 150 HOH HOH . 
G 4 HOH A 89 589 174 HOH HOH . 
G 4 HOH A 90 590 127 HOH HOH . 
G 4 HOH A 91 591 188 HOH HOH . 
G 4 HOH A 92 592 89 HOH HOH . 
G 4 HOH A 93 593 128 HOH HOH . 
G 4 HOH A 94 594 107 HOH HOH . 
G 4 HOH A 95 595 52 HOH HOH . 
G 4 HOH A 96 596 36 HOH HOH . 
G 4 HOH A 97 597 189 HOH HOH . 
G 4 HOH A 98 598 82 HOH HOH . 
G 4 HOH A 99 599 137 HOH HOH . 
H 4 HOH B 1 501 110 HOH HOH . 
H 4 HOH B 2 502 10 HOH HOH . 
H 4 HOH B 3 503 173 HOH HOH . 
H 4 HOH B 4 504 176 HOH HOH . 
H 4 HOH B 5 505 209 HOH HOH . 
H 4 HOH B 6 506 40 HOH HOH . 
H 4 HOH B 7 507 169 HOH HOH . 
H 4 HOH B 8 508 206 HOH HOH . 
H 4 HOH B 9 509 193 HOH HOH . 
H 4 HOH B 10 510 29 HOH HOH . 
H 4 HOH B 11 511 124 HOH HOH . 
H 4 HOH B 12 512 199 HOH HOH . 
H 4 HOH B 13 513 192 HOH HOH . 
H 4 HOH B 14 514 26 HOH HOH . 
H 4 HOH B 15 515 168 HOH HOH . 
H 4 HOH B 16 516 148 HOH HOH . 
H 4 HOH B 17 517 126 HOH HOH . 
H 4 HOH B 18 518 83 HOH HOH . 
H 4 HOH B 19 519 191 HOH HOH . 
H 4 HOH B 20 520 185 HOH HOH . 
H 4 HOH B 21 521 195 HOH HOH . 
H 4 HOH B 22 522 3 HOH HOH . 
H 4 HOH B 23 523 177 HOH HOH . 
H 4 HOH B 24 524 105 HOH HOH . 
H 4 HOH B 25 525 70 HOH HOH . 
H 4 HOH B 26 526 74 HOH HOH . 
H 4 HOH B 27 527 93 HOH HOH . 
H 4 HOH B 28 528 45 HOH HOH . 
H 4 HOH B 29 529 167 HOH HOH . 
H 4 HOH B 30 530 55 HOH HOH . 
H 4 HOH B 31 531 111 HOH HOH . 
H 4 HOH B 32 532 44 HOH HOH . 
H 4 HOH B 33 533 215 HOH HOH . 
H 4 HOH B 34 534 121 HOH HOH . 
H 4 HOH B 35 535 106 HOH HOH . 
H 4 HOH B 36 536 23 HOH HOH . 
H 4 HOH B 37 537 181 HOH HOH . 
H 4 HOH B 38 538 133 HOH HOH . 
H 4 HOH B 39 539 53 HOH HOH . 
H 4 HOH B 40 540 43 HOH HOH . 
H 4 HOH B 41 541 171 HOH HOH . 
H 4 HOH B 42 542 147 HOH HOH . 
H 4 HOH B 43 543 186 HOH HOH . 
H 4 HOH B 44 544 163 HOH HOH . 
H 4 HOH B 45 545 80 HOH HOH . 
H 4 HOH B 46 546 2 HOH HOH . 
H 4 HOH B 47 547 175 HOH HOH . 
H 4 HOH B 48 548 134 HOH HOH . 
H 4 HOH B 49 549 125 HOH HOH . 
H 4 HOH B 50 550 17 HOH HOH . 
H 4 HOH B 51 551 197 HOH HOH . 
H 4 HOH B 52 552 56 HOH HOH . 
H 4 HOH B 53 553 19 HOH HOH . 
H 4 HOH B 54 554 200 HOH HOH . 
H 4 HOH B 55 555 27 HOH HOH . 
H 4 HOH B 56 556 205 HOH HOH . 
H 4 HOH B 57 557 101 HOH HOH . 
H 4 HOH B 58 558 204 HOH HOH . 
H 4 HOH B 59 559 49 HOH HOH . 
H 4 HOH B 60 560 146 HOH HOH . 
H 4 HOH B 61 561 39 HOH HOH . 
H 4 HOH B 62 562 172 HOH HOH . 
H 4 HOH B 63 563 61 HOH HOH . 
H 4 HOH B 64 564 201 HOH HOH . 
H 4 HOH B 65 565 13 HOH HOH . 
H 4 HOH B 66 566 118 HOH HOH . 
H 4 HOH B 67 567 183 HOH HOH . 
H 4 HOH B 68 568 196 HOH HOH . 
H 4 HOH B 69 569 184 HOH HOH . 
H 4 HOH B 70 570 102 HOH HOH . 
H 4 HOH B 71 571 202 HOH HOH . 
H 4 HOH B 72 572 190 HOH HOH . 
H 4 HOH B 73 573 91 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 59.731 10.664 -1.673 1 26.77 ? N1 PLP 401 A 1 
HETATM 2 C C2 PLP . . . C 2 60.839 9.875 -1.483 1 30.3 ? C2 PLP 401 A 1 
HETATM 3 C C2A PLP . . . C 2 61.819 9.716 -2.608 1 34.8 ? C2A PLP 401 A 1 
HETATM 4 C C3 PLP . . . C 2 61.043 9.236 -0.266 1 31.82 ? C3 PLP 401 A 1 
HETATM 5 O O3 PLP . . . C 2 62.165 8.461 -0.122 1 31.94 ? O3 PLP 401 A 1 
HETATM 6 C C4 PLP . . . C 2 60.124 9.4 0.778 1 32.52 ? C4 PLP 401 A 1 
HETATM 7 C C4A PLP . . . C 2 60.36 8.751 2.117 1 29.2 ? C4A PLP 401 A 1 
HETATM 8 C C5 PLP . . . C 2 59.002 10.207 0.569 1 36.51 ? C5 PLP 401 A 1 
HETATM 9 C C6 PLP . . . C 2 58.812 10.816 -0.665 1 31.33 ? C6 PLP 401 A 1 
HETATM 10 C C5A PLP . . . C 2 57.918 10.423 1.604 1 35.35 ? C5A PLP 401 A 1 
HETATM 11 O O4P PLP . . . C 2 58.35 10.965 2.822 1 31.29 ? O4P PLP 401 A 1 
HETATM 12 P P PLP . . . C 2 57.231 11.243 3.953 1 29.16 ? P PLP 401 A 1 
HETATM 13 O O1P PLP . . . C 2 55.837 11.172 3.391 1 26.28 -1 O1P PLP 401 A 1 
HETATM 14 O O2P PLP . . . C 2 57.364 10.182 5.017 1 32.31 ? O2P PLP 401 A 1 
HETATM 15 O O3P PLP . . . C 2 57.447 12.626 4.527 1 31.36 ? O3P PLP 401 A 1 
HETATM 16 H H2A1 PLP . . . C 2 62.637 9.071 -2.288 1 41.76 ? H2A1 PLP 401 A 1 
HETATM 17 H H2A2 PLP . . . C 2 62.213 10.693 -2.887 1 41.76 ? H2A2 PLP 401 A 1 
HETATM 18 H H2A3 PLP . . . C 2 61.317 9.268 -3.466 1 41.76 ? H2A3 PLP 401 A 1 
HETATM 19 H HO3 PLP . . . C 2 62.176 8.066 0.775 1 38.32 ? HO3 PLP 401 A 1 
HETATM 20 H H6 PLP . . . C 2 57.922 11.423 -0.835 1 37.6 ? H6 PLP 401 A 1 
HETATM 21 H H5A1 PLP . . . C 2 57.442 9.463 1.806 1 42.42 ? H5A1 PLP 401 A 1 
HETATM 22 H H5A2 PLP . . . C 2 57.166 11.088 1.18 1 42.42 ? H5A2 PLP 401 A 1 
#
_model_server_stats.io_time_ms              30 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           281 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           22 
#