data_5I7R
#
_model_server_result.job_id            qroGE1VjLapTc0AxEV6VtQ 
_model_server_result.datetime_utc      '2024-12-21 15:08:11' 
_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          5i7r 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":401}' 
#
_entry.id    5I7R 
#
_exptl.entry_id    5I7R 
_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         90 
_cell.entry_id            5I7R 
_cell.length_a            72.17 
_cell.length_b            86.487 
_cell.length_c            101.584 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5I7R 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_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,I,J,K,L,M 
_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 H 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 54 B LYS 51 1_555 C C4A PLP . B PLP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.389 ? 
covale ? covale2 B NZ LYS 54 A LYS 51 1_555 H C4A PLP . A PLP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.382 ? 
#
_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 309 n y 
N1 C6 PLP sing 310 n y 
C2 C2A PLP sing 311 n n 
C2 C3 PLP sing 312 n y 
C2A H2A1 PLP sing 313 n n 
C2A H2A2 PLP sing 314 n n 
C2A H2A3 PLP sing 315 n n 
C3 O3 PLP sing 316 n n 
C3 C4 PLP doub 317 n y 
O3 HO3 PLP sing 318 n n 
C4 C4A PLP sing 319 n n 
C4 C5 PLP sing 320 n y 
C4A O4A PLP doub 321 n n 
C4A H4A PLP sing 322 n n 
C5 C6 PLP doub 323 n y 
C5 C5A PLP sing 324 n n 
C6 H6 PLP sing 325 n n 
C5A O4P PLP sing 326 n n 
C5A H5A1 PLP sing 327 n n 
C5A H5A2 PLP sing 328 n n 
O4P P PLP sing 329 n n 
P O1P PLP doub 330 n n 
P O2P PLP sing 331 n n 
P O3P PLP sing 332 n n 
O2P HOP2 PLP sing 333 n n 
O3P HOP3 PLP sing 334 n n 
#
_atom_sites.entry_id                     5I7R 
_atom_sites.fract_transf_matrix[1][1]    0.013856 
_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]    0.011562 
_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]    0.009844 
_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 B 1 401 51 PLP LLP . 
D 3 68W B 1 402 2 68W 51G . 
E 4 ACT B 1 403 2 ACT ACT . 
F 4 ACT B 1 404 3 ACT ACT . 
G 4 ACT B 1 405 6 ACT ACT . 
H 2 PLP A 1 401 51 PLP LLP . 
I 3 68W A 1 402 1 68W 51G . 
J 4 ACT A 1 403 1 ACT ACT . 
K 4 ACT A 1 404 4 ACT ACT . 
L 5 HOH B 1 501 327 HOH HOH . 
L 5 HOH B 2 502 72 HOH HOH . 
L 5 HOH B 3 503 214 HOH HOH . 
L 5 HOH B 4 504 324 HOH HOH . 
L 5 HOH B 5 505 200 HOH HOH . 
L 5 HOH B 6 506 154 HOH HOH . 
L 5 HOH B 7 507 51 HOH HOH . 
L 5 HOH B 8 508 337 HOH HOH . 
L 5 HOH B 9 509 109 HOH HOH . 
L 5 HOH B 10 510 10 HOH HOH . 
L 5 HOH B 11 511 46 HOH HOH . 
L 5 HOH B 12 512 33 HOH HOH . 
L 5 HOH B 13 513 122 HOH HOH . 
L 5 HOH B 14 514 39 HOH HOH . 
L 5 HOH B 15 515 301 HOH HOH . 
L 5 HOH B 16 516 65 HOH HOH . 
L 5 HOH B 17 517 18 HOH HOH . 
L 5 HOH B 18 518 146 HOH HOH . 
L 5 HOH B 19 519 107 HOH HOH . 
L 5 HOH B 20 520 79 HOH HOH . 
L 5 HOH B 21 521 294 HOH HOH . 
L 5 HOH B 22 522 345 HOH HOH . 
L 5 HOH B 23 523 7 HOH HOH . 
L 5 HOH B 24 524 116 HOH HOH . 
L 5 HOH B 25 525 68 HOH HOH . 
L 5 HOH B 26 526 115 HOH HOH . 
L 5 HOH B 27 527 110 HOH HOH . 
L 5 HOH B 28 528 349 HOH HOH . 
L 5 HOH B 29 529 80 HOH HOH . 
L 5 HOH B 30 530 35 HOH HOH . 
L 5 HOH B 31 531 169 HOH HOH . 
L 5 HOH B 32 532 78 HOH HOH . 
L 5 HOH B 33 533 158 HOH HOH . 
L 5 HOH B 34 534 213 HOH HOH . 
L 5 HOH B 35 535 212 HOH HOH . 
L 5 HOH B 36 536 36 HOH HOH . 
L 5 HOH B 37 537 16 HOH HOH . 
L 5 HOH B 38 538 276 HOH HOH . 
L 5 HOH B 39 539 136 HOH HOH . 
L 5 HOH B 40 540 149 HOH HOH . 
L 5 HOH B 41 541 60 HOH HOH . 
L 5 HOH B 42 542 28 HOH HOH . 
L 5 HOH B 43 543 50 HOH HOH . 
L 5 HOH B 44 544 339 HOH HOH . 
L 5 HOH B 45 545 66 HOH HOH . 
L 5 HOH B 46 546 334 HOH HOH . 
L 5 HOH B 47 547 266 HOH HOH . 
L 5 HOH B 48 548 3 HOH HOH . 
L 5 HOH B 49 549 218 HOH HOH . 
L 5 HOH B 50 550 40 HOH HOH . 
L 5 HOH B 51 551 330 HOH HOH . 
L 5 HOH B 52 552 94 HOH HOH . 
L 5 HOH B 53 553 24 HOH HOH . 
L 5 HOH B 54 554 83 HOH HOH . 
L 5 HOH B 55 555 167 HOH HOH . 
L 5 HOH B 56 556 342 HOH HOH . 
L 5 HOH B 57 557 189 HOH HOH . 
L 5 HOH B 58 558 341 HOH HOH . 
L 5 HOH B 59 559 117 HOH HOH . 
L 5 HOH B 60 560 67 HOH HOH . 
L 5 HOH B 61 561 295 HOH HOH . 
L 5 HOH B 62 562 156 HOH HOH . 
L 5 HOH B 63 563 230 HOH HOH . 
L 5 HOH B 64 564 61 HOH HOH . 
L 5 HOH B 65 565 21 HOH HOH . 
L 5 HOH B 66 566 205 HOH HOH . 
L 5 HOH B 67 567 331 HOH HOH . 
L 5 HOH B 68 568 292 HOH HOH . 
L 5 HOH B 69 569 100 HOH HOH . 
L 5 HOH B 70 570 101 HOH HOH . 
L 5 HOH B 71 571 93 HOH HOH . 
L 5 HOH B 72 572 112 HOH HOH . 
L 5 HOH B 73 573 92 HOH HOH . 
L 5 HOH B 74 574 219 HOH HOH . 
L 5 HOH B 75 575 283 HOH HOH . 
L 5 HOH B 76 576 138 HOH HOH . 
L 5 HOH B 77 577 47 HOH HOH . 
L 5 HOH B 78 578 270 HOH HOH . 
L 5 HOH B 79 579 20 HOH HOH . 
L 5 HOH B 80 580 303 HOH HOH . 
L 5 HOH B 81 581 87 HOH HOH . 
L 5 HOH B 82 582 131 HOH HOH . 
L 5 HOH B 83 583 231 HOH HOH . 
L 5 HOH B 84 584 106 HOH HOH . 
L 5 HOH B 85 585 174 HOH HOH . 
L 5 HOH B 86 586 188 HOH HOH . 
L 5 HOH B 87 587 226 HOH HOH . 
L 5 HOH B 88 588 151 HOH HOH . 
L 5 HOH B 89 589 233 HOH HOH . 
L 5 HOH B 90 590 157 HOH HOH . 
L 5 HOH B 91 591 267 HOH HOH . 
L 5 HOH B 92 592 287 HOH HOH . 
L 5 HOH B 93 593 187 HOH HOH . 
L 5 HOH B 94 594 348 HOH HOH . 
L 5 HOH B 95 595 132 HOH HOH . 
L 5 HOH B 96 596 95 HOH HOH . 
L 5 HOH B 97 597 186 HOH HOH . 
L 5 HOH B 98 598 171 HOH HOH . 
L 5 HOH B 99 599 176 HOH HOH . 
L 5 HOH B 100 600 329 HOH HOH . 
L 5 HOH B 101 601 175 HOH HOH . 
L 5 HOH B 102 602 111 HOH HOH . 
L 5 HOH B 103 603 282 HOH HOH . 
L 5 HOH B 104 604 344 HOH HOH . 
L 5 HOH B 105 605 346 HOH HOH . 
L 5 HOH B 106 606 265 HOH HOH . 
L 5 HOH B 107 607 208 HOH HOH . 
L 5 HOH B 108 608 178 HOH HOH . 
L 5 HOH B 109 609 300 HOH HOH . 
M 5 HOH A 1 501 277 HOH HOH . 
M 5 HOH A 2 502 62 HOH HOH . 
M 5 HOH A 3 503 76 HOH HOH . 
M 5 HOH A 4 504 140 HOH HOH . 
M 5 HOH A 5 505 161 HOH HOH . 
M 5 HOH A 6 506 166 HOH HOH . 
M 5 HOH A 7 507 84 HOH HOH . 
M 5 HOH A 8 508 54 HOH HOH . 
M 5 HOH A 9 509 273 HOH HOH . 
M 5 HOH A 10 510 81 HOH HOH . 
M 5 HOH A 11 511 147 HOH HOH . 
M 5 HOH A 12 512 43 HOH HOH . 
M 5 HOH A 13 513 69 HOH HOH . 
M 5 HOH A 14 514 57 HOH HOH . 
M 5 HOH A 15 515 25 HOH HOH . 
M 5 HOH A 16 516 27 HOH HOH . 
M 5 HOH A 17 517 12 HOH HOH . 
M 5 HOH A 18 518 203 HOH HOH . 
M 5 HOH A 19 519 29 HOH HOH . 
M 5 HOH A 20 520 141 HOH HOH . 
M 5 HOH A 21 521 113 HOH HOH . 
M 5 HOH A 22 522 91 HOH HOH . 
M 5 HOH A 23 523 34 HOH HOH . 
M 5 HOH A 24 524 286 HOH HOH . 
M 5 HOH A 25 525 235 HOH HOH . 
M 5 HOH A 26 526 44 HOH HOH . 
M 5 HOH A 27 527 216 HOH HOH . 
M 5 HOH A 28 528 335 HOH HOH . 
M 5 HOH A 29 529 227 HOH HOH . 
M 5 HOH A 30 530 4 HOH HOH . 
M 5 HOH A 31 531 121 HOH HOH . 
M 5 HOH A 32 532 45 HOH HOH . 
M 5 HOH A 33 533 168 HOH HOH . 
M 5 HOH A 34 534 49 HOH HOH . 
M 5 HOH A 35 535 64 HOH HOH . 
M 5 HOH A 36 536 119 HOH HOH . 
M 5 HOH A 37 537 114 HOH HOH . 
M 5 HOH A 38 538 99 HOH HOH . 
M 5 HOH A 39 539 336 HOH HOH . 
M 5 HOH A 40 540 23 HOH HOH . 
M 5 HOH A 41 541 197 HOH HOH . 
M 5 HOH A 42 542 48 HOH HOH . 
M 5 HOH A 43 543 211 HOH HOH . 
M 5 HOH A 44 544 172 HOH HOH . 
M 5 HOH A 45 545 120 HOH HOH . 
M 5 HOH A 46 546 285 HOH HOH . 
M 5 HOH A 47 547 262 HOH HOH . 
M 5 HOH A 48 548 75 HOH HOH . 
M 5 HOH A 49 549 343 HOH HOH . 
M 5 HOH A 50 550 260 HOH HOH . 
M 5 HOH A 51 551 284 HOH HOH . 
M 5 HOH A 52 552 332 HOH HOH . 
M 5 HOH A 53 553 340 HOH HOH . 
M 5 HOH A 54 554 278 HOH HOH . 
M 5 HOH A 55 555 143 HOH HOH . 
M 5 HOH A 56 556 26 HOH HOH . 
M 5 HOH A 57 557 31 HOH HOH . 
M 5 HOH A 58 558 159 HOH HOH . 
M 5 HOH A 59 559 37 HOH HOH . 
M 5 HOH A 60 560 333 HOH HOH . 
M 5 HOH A 61 561 19 HOH HOH . 
M 5 HOH A 62 562 196 HOH HOH . 
M 5 HOH A 63 563 297 HOH HOH . 
M 5 HOH A 64 564 153 HOH HOH . 
M 5 HOH A 65 565 130 HOH HOH . 
M 5 HOH A 66 566 42 HOH HOH . 
M 5 HOH A 67 567 179 HOH HOH . 
M 5 HOH A 68 568 118 HOH HOH . 
M 5 HOH A 69 569 70 HOH HOH . 
M 5 HOH A 70 570 77 HOH HOH . 
M 5 HOH A 71 571 139 HOH HOH . 
M 5 HOH A 72 572 90 HOH HOH . 
M 5 HOH A 73 573 302 HOH HOH . 
M 5 HOH A 74 574 328 HOH HOH . 
M 5 HOH A 75 575 269 HOH HOH . 
M 5 HOH A 76 576 108 HOH HOH . 
M 5 HOH A 77 577 103 HOH HOH . 
M 5 HOH A 78 578 160 HOH HOH . 
M 5 HOH A 79 579 261 HOH HOH . 
M 5 HOH A 80 580 293 HOH HOH . 
M 5 HOH A 81 581 124 HOH HOH . 
M 5 HOH A 82 582 350 HOH HOH . 
M 5 HOH A 83 583 298 HOH HOH . 
M 5 HOH A 84 584 304 HOH HOH . 
M 5 HOH A 85 585 299 HOH HOH . 
M 5 HOH A 86 586 180 HOH HOH . 
M 5 HOH A 87 587 182 HOH HOH . 
M 5 HOH A 88 588 338 HOH HOH . 
M 5 HOH A 89 589 272 HOH HOH . 
M 5 HOH A 90 590 252 HOH HOH . 
M 5 HOH A 91 591 290 HOH HOH . 
M 5 HOH A 92 592 210 HOH HOH . 
M 5 HOH A 93 593 289 HOH HOH . 
M 5 HOH A 94 594 296 HOH HOH . 
M 5 HOH A 95 595 97 HOH HOH . 
M 5 HOH A 96 596 183 HOH HOH . 
M 5 HOH A 97 597 288 HOH HOH . 
M 5 HOH A 98 598 236 HOH HOH . 
M 5 HOH A 99 599 347 HOH HOH . 
M 5 HOH A 100 600 275 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 . . . H 2 3.846 6.188 6.076 1 23.37 ? N1 PLP 401 A 1 
HETATM 2 C C2 PLP . . . H 2 3.528 5.101 6.8 1 20.93 ? C2 PLP 401 A 1 
HETATM 3 C C2A PLP . . . H 2 3.007 5.205 8.223 1 20.28 ? C2A PLP 401 A 1 
HETATM 4 C C3 PLP . . . H 2 3.678 3.76 6.229 1 21.13 ? C3 PLP 401 A 1 
HETATM 5 O O3 PLP . . . H 2 3.351 2.65 6.915 1 24.49 ? O3 PLP 401 A 1 
HETATM 6 C C4 PLP . . . H 2 4.155 3.655 4.852 1 20.53 ? C4 PLP 401 A 1 
HETATM 7 C C4A PLP . . . H 2 4.326 2.353 4.193 1 21.03 ? C4A PLP 401 A 1 
HETATM 8 C C5 PLP . . . H 2 4.505 4.883 4.163 1 22.98 ? C5 PLP 401 A 1 
HETATM 9 C C6 PLP . . . H 2 4.311 6.099 4.793 1 23.58 ? C6 PLP 401 A 1 
HETATM 10 C C5A PLP . . . H 2 5.055 4.831 2.739 1 22.99 ? C5A PLP 401 A 1 
HETATM 11 O O4P PLP . . . H 2 4.182 4.208 1.824 1 21.98 ? O4P PLP 401 A 1 
HETATM 12 P P PLP . . . H 2 4.829 3.209 0.705 1 22.23 ? P PLP 401 A 1 
HETATM 13 O O1P PLP . . . H 2 3.657 2.86 -0.15 1 21.37 ? O1P PLP 401 A 1 
HETATM 14 O O2P PLP . . . H 2 5.494 2.025 1.348 1 22.32 ? O2P PLP 401 A 1 
HETATM 15 O O3P PLP . . . H 2 5.875 3.996 -0.122 1 22.63 ? O3P PLP 401 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    25 
_model_server_stats.query_time_ms           274 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           15 
#