data_5B87
#
_model_server_result.job_id            oNLEWFI809DzSgo-vzYo7A 
_model_server_result.datetime_utc      '2025-01-02 18:47:37' 
_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          5b87 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":400}' 
#
_entry.id    5B87 
#
_exptl.entry_id    5B87 
_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            5B87 
_cell.length_a            67.282 
_cell.length_b            93.809 
_cell.length_c            145.534 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5B87 
_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 
_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 E 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 236 A LYS 216 1_555 C C4A PLP . A PLP 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? 
covale ? covale2 A C HIS 375 A HIS 355 1_555 A N CSS 376 A CSS 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.31 ? 
covale ? covale3 A C CSS 376 A CSS 356 1_555 A N ALA 377 A ALA 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? 
covale ? covale4 C C4A PLP . A PLP 400 1_555 D N ALA . A ALA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.511 ? 
covale ? covale5 B NZ LYS 236 B LYS 216 1_555 E C4A PLP . B PLP 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.513 ? 
covale ? covale6 B C HIS 375 B HIS 355 1_555 B N CSS 376 B CSS 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? 
covale ? covale7 B C CSS 376 B CSS 356 1_555 B N ALA 377 B ALA 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.314 ? 
covale ? covale8 E C4A PLP . B PLP 400 1_555 F N ALA . B ALA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.532 ? 
#
_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 261 n y 
N1 C6 PLP sing 262 n y 
C2 C2A PLP sing 263 n n 
C2 C3 PLP sing 264 n y 
C2A H2A1 PLP sing 265 n n 
C2A H2A2 PLP sing 266 n n 
C2A H2A3 PLP sing 267 n n 
C3 O3 PLP sing 268 n n 
C3 C4 PLP doub 269 n y 
O3 HO3 PLP sing 270 n n 
C4 C4A PLP sing 271 n n 
C4 C5 PLP sing 272 n y 
C4A O4A PLP doub 273 n n 
C4A H4A PLP sing 274 n n 
C5 C6 PLP doub 275 n y 
C5 C5A PLP sing 276 n n 
C6 H6 PLP sing 277 n n 
C5A O4P PLP sing 278 n n 
C5A H5A1 PLP sing 279 n n 
C5A H5A2 PLP sing 280 n n 
O4P P PLP sing 281 n n 
P O1P PLP doub 282 n n 
P O2P PLP sing 283 n n 
P O3P PLP sing 284 n n 
O2P HOP2 PLP sing 285 n n 
O3P HOP3 PLP sing 286 n n 
#
_atom_sites.entry_id                     5B87 
_atom_sites.fract_transf_matrix[1][1]    0.014863 
_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]    0.01066 
_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]    0.006871 
_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 1 400 400 PLP PLP . 
D 3 ALA A 1 401 401 ALA ALA . 
E 2 PLP B 1 400 400 PLP PLP . 
F 3 ALA B 1 401 401 ALA ALA . 
G 4 HOH A 1 501 501 HOH HOH . 
G 4 HOH A 2 502 502 HOH HOH . 
G 4 HOH A 3 503 503 HOH HOH . 
G 4 HOH A 4 504 504 HOH HOH . 
G 4 HOH A 5 505 505 HOH HOH . 
G 4 HOH A 6 506 506 HOH HOH . 
G 4 HOH A 7 507 507 HOH HOH . 
G 4 HOH A 8 508 508 HOH HOH . 
G 4 HOH A 9 509 509 HOH HOH . 
G 4 HOH A 10 510 510 HOH HOH . 
G 4 HOH A 11 511 511 HOH HOH . 
G 4 HOH A 12 512 512 HOH HOH . 
G 4 HOH A 13 513 513 HOH HOH . 
G 4 HOH A 14 514 514 HOH HOH . 
G 4 HOH A 15 515 515 HOH HOH . 
G 4 HOH A 16 516 516 HOH HOH . 
G 4 HOH A 17 517 517 HOH HOH . 
G 4 HOH A 18 518 518 HOH HOH . 
G 4 HOH A 19 519 519 HOH HOH . 
G 4 HOH A 20 520 520 HOH HOH . 
G 4 HOH A 21 521 521 HOH HOH . 
G 4 HOH A 22 522 522 HOH HOH . 
G 4 HOH A 23 523 523 HOH HOH . 
G 4 HOH A 24 524 524 HOH HOH . 
G 4 HOH A 25 525 525 HOH HOH . 
G 4 HOH A 26 526 526 HOH HOH . 
G 4 HOH A 27 527 527 HOH HOH . 
G 4 HOH A 28 528 528 HOH HOH . 
G 4 HOH A 29 529 529 HOH HOH . 
G 4 HOH A 30 530 530 HOH HOH . 
G 4 HOH A 31 531 531 HOH HOH . 
G 4 HOH A 32 532 532 HOH HOH . 
G 4 HOH A 33 533 533 HOH HOH . 
G 4 HOH A 34 534 534 HOH HOH . 
G 4 HOH A 35 535 535 HOH HOH . 
G 4 HOH A 36 536 538 HOH HOH . 
G 4 HOH A 37 537 536 HOH HOH . 
G 4 HOH A 38 538 537 HOH HOH . 
G 4 HOH A 39 539 539 HOH HOH . 
G 4 HOH A 40 540 540 HOH HOH . 
G 4 HOH A 41 541 541 HOH HOH . 
G 4 HOH A 42 542 542 HOH HOH . 
G 4 HOH A 43 543 543 HOH HOH . 
G 4 HOH A 44 544 544 HOH HOH . 
G 4 HOH A 45 545 545 HOH HOH . 
G 4 HOH A 46 546 546 HOH HOH . 
G 4 HOH A 47 547 547 HOH HOH . 
G 4 HOH A 48 548 548 HOH HOH . 
G 4 HOH A 49 549 549 HOH HOH . 
G 4 HOH A 50 550 550 HOH HOH . 
G 4 HOH A 51 551 551 HOH HOH . 
G 4 HOH A 52 552 552 HOH HOH . 
G 4 HOH A 53 553 553 HOH HOH . 
G 4 HOH A 54 554 554 HOH HOH . 
G 4 HOH A 55 555 555 HOH HOH . 
G 4 HOH A 56 556 556 HOH HOH . 
G 4 HOH A 57 557 557 HOH HOH . 
G 4 HOH A 58 558 558 HOH HOH . 
G 4 HOH A 59 559 559 HOH HOH . 
G 4 HOH A 60 560 560 HOH HOH . 
G 4 HOH A 61 561 561 HOH HOH . 
G 4 HOH A 62 562 562 HOH HOH . 
G 4 HOH A 63 563 563 HOH HOH . 
G 4 HOH A 64 564 564 HOH HOH . 
G 4 HOH A 65 565 565 HOH HOH . 
G 4 HOH A 66 566 566 HOH HOH . 
G 4 HOH A 67 567 567 HOH HOH . 
G 4 HOH A 68 568 568 HOH HOH . 
H 4 HOH B 1 501 501 HOH HOH . 
H 4 HOH B 2 502 502 HOH HOH . 
H 4 HOH B 3 503 503 HOH HOH . 
H 4 HOH B 4 504 504 HOH HOH . 
H 4 HOH B 5 505 505 HOH HOH . 
H 4 HOH B 6 506 506 HOH HOH . 
H 4 HOH B 7 507 507 HOH HOH . 
H 4 HOH B 8 508 508 HOH HOH . 
H 4 HOH B 9 509 509 HOH HOH . 
H 4 HOH B 10 510 510 HOH HOH . 
H 4 HOH B 11 511 511 HOH HOH . 
H 4 HOH B 12 512 512 HOH HOH . 
H 4 HOH B 13 513 513 HOH HOH . 
H 4 HOH B 14 514 514 HOH HOH . 
H 4 HOH B 15 515 515 HOH HOH . 
H 4 HOH B 16 516 516 HOH HOH . 
H 4 HOH B 17 517 517 HOH HOH . 
H 4 HOH B 18 518 518 HOH HOH . 
H 4 HOH B 19 519 519 HOH HOH . 
H 4 HOH B 20 520 520 HOH HOH . 
H 4 HOH B 21 521 521 HOH HOH . 
H 4 HOH B 22 522 522 HOH HOH . 
H 4 HOH B 23 523 523 HOH HOH . 
H 4 HOH B 24 524 524 HOH HOH . 
H 4 HOH B 25 525 525 HOH HOH . 
H 4 HOH B 26 526 526 HOH HOH . 
H 4 HOH B 27 527 527 HOH HOH . 
H 4 HOH B 28 528 528 HOH HOH . 
H 4 HOH B 29 529 529 HOH HOH . 
H 4 HOH B 30 530 530 HOH HOH . 
H 4 HOH B 31 531 531 HOH HOH . 
H 4 HOH B 32 532 532 HOH HOH . 
H 4 HOH B 33 533 533 HOH HOH . 
H 4 HOH B 34 534 534 HOH HOH . 
H 4 HOH B 35 535 535 HOH HOH . 
H 4 HOH B 36 536 536 HOH HOH . 
H 4 HOH B 37 537 537 HOH HOH . 
H 4 HOH B 38 538 538 HOH HOH . 
H 4 HOH B 39 539 539 HOH HOH . 
H 4 HOH B 40 540 547 HOH HOH . 
H 4 HOH B 41 541 540 HOH HOH . 
H 4 HOH B 42 542 541 HOH HOH . 
H 4 HOH B 43 543 542 HOH HOH . 
H 4 HOH B 44 544 543 HOH HOH . 
H 4 HOH B 45 545 544 HOH HOH . 
H 4 HOH B 46 546 545 HOH HOH . 
H 4 HOH B 47 547 546 HOH HOH . 
H 4 HOH B 48 548 548 HOH HOH . 
H 4 HOH B 49 549 549 HOH HOH . 
H 4 HOH B 50 550 550 HOH HOH . 
H 4 HOH B 51 551 551 HOH HOH . 
H 4 HOH B 52 552 552 HOH HOH . 
H 4 HOH B 53 553 553 HOH HOH . 
H 4 HOH B 54 554 554 HOH HOH . 
H 4 HOH B 55 555 555 HOH HOH . 
H 4 HOH B 56 556 556 HOH HOH . 
H 4 HOH B 57 557 557 HOH HOH . 
H 4 HOH B 58 558 558 HOH HOH . 
H 4 HOH B 59 559 559 HOH HOH . 
H 4 HOH B 60 560 560 HOH HOH . 
H 4 HOH B 61 561 561 HOH HOH . 
H 4 HOH B 62 562 562 HOH HOH . 
H 4 HOH B 63 563 563 HOH HOH . 
H 4 HOH B 64 564 564 HOH HOH . 
H 4 HOH B 65 565 565 HOH HOH . 
H 4 HOH B 66 566 566 HOH HOH . 
H 4 HOH B 67 567 567 HOH HOH . 
H 4 HOH B 68 568 568 HOH HOH . 
H 4 HOH B 69 569 569 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 44.288 0.27 -11.057 1 28.44 ? N1 PLP 400 A 1 
HETATM 2 C C2 PLP . . . C 2 43.859 0.819 -12.189 1 43.52 ? C2 PLP 400 A 1 
HETATM 3 C C2A PLP . . . C 2 44.414 0.117 -13.43 1 44.36 ? C2A PLP 400 A 1 
HETATM 4 C C3 PLP . . . C 2 42.968 1.947 -12.257 1 33.64 ? C3 PLP 400 A 1 
HETATM 5 O O3 PLP . . . C 2 42.491 2.595 -13.448 1 41.85 ? O3 PLP 400 A 1 
HETATM 6 C C4 PLP . . . C 2 42.536 2.458 -11.081 1 35.4 ? C4 PLP 400 A 1 
HETATM 7 C C4A PLP . . . C 2 41.597 3.751 -11.183 1 44.33 ? C4A PLP 400 A 1 
HETATM 8 C C5 PLP . . . C 2 43.022 1.927 -9.889 1 27.44 ? C5 PLP 400 A 1 
HETATM 9 C C6 PLP . . . C 2 43.84 0.812 -9.916 1 30.33 ? C6 PLP 400 A 1 
HETATM 10 C C5A PLP . . . C 2 42.554 2.448 -8.567 1 29.84 ? C5A PLP 400 A 1 
HETATM 11 O O4P PLP . . . C 2 41.117 2.182 -8.485 1 29.17 ? O4P PLP 400 A 1 
HETATM 12 P P PLP . . . C 2 40.313 3.159 -7.421 1 28.34 ? P PLP 400 A 1 
HETATM 13 O O1P PLP . . . C 2 38.872 2.935 -7.549 1 29.46 -1 O1P PLP 400 A 1 
HETATM 14 O O2P PLP . . . C 2 40.921 2.828 -6.141 1 24.22 ? O2P PLP 400 A 1 
HETATM 15 O O3P PLP . . . C 2 40.664 4.634 -7.476 1 25.5 -1 O3P PLP 400 A 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    16 
_model_server_stats.query_time_ms           318 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           15 
#