data_7NEB
#
_model_server_result.job_id            IizTbRy8J-m6vurJ_LM81A 
_model_server_result.datetime_utc      '2024-11-28 23:03:27' 
_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          7neb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":401}' 
#
_entry.id    7NEB 
#
_exptl.entry_id    7NEB 
_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            7NEB 
_cell.length_a            146.02 
_cell.length_b            146.02 
_cell.length_c            142.115 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7NEB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        155 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'H 3 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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    1,2,3,4,5,6 
#
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' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 146.02 0 0 
3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 73.01 126.457029 0 
4 'crystal symmetry operation' 16_545 y+1/3,x-1/3,-z+2/3 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 73.01 -42.152343 94.743333 
5 'crystal symmetry operation' 17_555 x-y+1/3,-y+2/3,-z+2/3 1 0 0 0 -1 0 0 0 -1 0 84.304686 94.743333 
6 'crystal symmetry operation' 18_655 -x+4/3,-x+y+2/3,-z+2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 146.02 84.304686 94.743333 
#
_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 
#
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
disulf ? disulf1 A SG CYS 199 A CYS 200 1_555 A SG CYS 257 A CYS 258 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.072 ? 
covale ? covale1 A NZ LYS 160 A LYS 161 1_555 B C4A PLP . A PLP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.242 ? 
#
_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                     7NEB 
_atom_sites.fract_transf_matrix[1][1]    0.006848 
_atom_sites.fract_transf_matrix[1][2]    0.003954 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007908 
_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]    0.007037 
_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 1 401 401 PLP PLP . 
C 3 NA A 1 402 1 NA NA . 
D 4 HOH A 1 501 87 HOH HOH . 
D 4 HOH A 2 502 86 HOH HOH . 
D 4 HOH A 3 503 30 HOH HOH . 
D 4 HOH A 4 504 1 HOH HOH . 
D 4 HOH A 5 505 15 HOH HOH . 
D 4 HOH A 6 506 85 HOH HOH . 
D 4 HOH A 7 507 28 HOH HOH . 
D 4 HOH A 8 508 102 HOH HOH . 
D 4 HOH A 9 509 36 HOH HOH . 
D 4 HOH A 10 510 39 HOH HOH . 
D 4 HOH A 11 511 79 HOH HOH . 
D 4 HOH A 12 512 21 HOH HOH . 
D 4 HOH A 13 513 10 HOH HOH . 
D 4 HOH A 14 514 98 HOH HOH . 
D 4 HOH A 15 515 9 HOH HOH . 
D 4 HOH A 16 516 91 HOH HOH . 
D 4 HOH A 17 517 40 HOH HOH . 
D 4 HOH A 18 518 16 HOH HOH . 
D 4 HOH A 19 519 100 HOH HOH . 
D 4 HOH A 20 520 61 HOH HOH . 
D 4 HOH A 21 521 43 HOH HOH . 
D 4 HOH A 22 522 22 HOH HOH . 
D 4 HOH A 23 523 20 HOH HOH . 
D 4 HOH A 24 524 6 HOH HOH . 
D 4 HOH A 25 525 88 HOH HOH . 
D 4 HOH A 26 526 90 HOH HOH . 
D 4 HOH A 27 527 28 HOH HOH . 
D 4 HOH A 28 528 53 HOH HOH . 
D 4 HOH A 29 529 32 HOH HOH . 
D 4 HOH A 30 530 14 HOH HOH . 
D 4 HOH A 31 531 24 HOH HOH . 
D 4 HOH A 32 532 7 HOH HOH . 
D 4 HOH A 33 533 30 HOH HOH . 
D 4 HOH A 34 534 99 HOH HOH . 
D 4 HOH A 35 535 39 HOH HOH . 
D 4 HOH A 36 536 64 HOH HOH . 
D 4 HOH A 37 537 7 HOH HOH . 
D 4 HOH A 38 538 37 HOH HOH . 
D 4 HOH A 39 539 74 HOH HOH . 
D 4 HOH A 40 540 27 HOH HOH . 
D 4 HOH A 41 541 108 HOH HOH . 
D 4 HOH A 42 542 43 HOH HOH . 
D 4 HOH A 43 543 31 HOH HOH . 
D 4 HOH A 44 544 9 HOH HOH . 
D 4 HOH A 45 545 2 HOH HOH . 
D 4 HOH A 46 546 38 HOH HOH . 
D 4 HOH A 47 547 101 HOH HOH . 
D 4 HOH A 48 548 5 HOH HOH . 
D 4 HOH A 49 549 13 HOH HOH . 
D 4 HOH A 50 550 35 HOH HOH . 
D 4 HOH A 51 551 114 HOH HOH . 
D 4 HOH A 52 552 37 HOH HOH . 
D 4 HOH A 53 553 76 HOH HOH . 
D 4 HOH A 54 554 97 HOH HOH . 
D 4 HOH A 55 555 109 HOH HOH . 
D 4 HOH A 56 556 111 HOH HOH . 
D 4 HOH A 57 557 21 HOH HOH . 
D 4 HOH A 58 558 41 HOH HOH . 
D 4 HOH A 59 559 106 HOH HOH . 
D 4 HOH A 60 560 110 HOH HOH . 
D 4 HOH A 61 561 32 HOH HOH . 
D 4 HOH A 62 562 81 HOH HOH . 
D 4 HOH A 63 563 122 HOH HOH . 
D 4 HOH A 64 564 17 HOH HOH . 
D 4 HOH A 65 565 29 HOH HOH . 
D 4 HOH A 66 566 105 HOH HOH . 
D 4 HOH A 67 567 121 HOH HOH . 
D 4 HOH A 68 568 120 HOH HOH . 
D 4 HOH A 69 569 92 HOH HOH . 
D 4 HOH A 70 570 8 HOH HOH . 
D 4 HOH A 71 571 116 HOH HOH . 
D 4 HOH A 72 572 118 HOH HOH . 
D 4 HOH A 73 573 16 HOH HOH . 
D 4 HOH A 74 574 33 HOH HOH . 
D 4 HOH A 75 575 46 HOH HOH . 
D 4 HOH A 76 576 38 HOH HOH . 
D 4 HOH A 77 577 25 HOH HOH . 
D 4 HOH A 78 578 77 HOH HOH . 
D 4 HOH A 79 579 33 HOH HOH . 
D 4 HOH A 80 580 84 HOH HOH . 
D 4 HOH A 81 581 103 HOH HOH . 
D 4 HOH A 82 582 57 HOH HOH . 
D 4 HOH A 83 583 115 HOH HOH . 
D 4 HOH A 84 584 14 HOH HOH . 
D 4 HOH A 85 585 19 HOH HOH . 
D 4 HOH A 86 586 104 HOH HOH . 
D 4 HOH A 87 587 78 HOH HOH . 
D 4 HOH A 88 588 18 HOH HOH . 
D 4 HOH A 89 589 107 HOH HOH . 
D 4 HOH A 90 590 42 HOH HOH . 
D 4 HOH A 91 591 10 HOH HOH . 
D 4 HOH A 92 592 75 HOH HOH . 
D 4 HOH A 93 593 36 HOH HOH . 
D 4 HOH A 94 594 8 HOH HOH . 
D 4 HOH A 95 595 62 HOH HOH . 
D 4 HOH A 96 596 83 HOH HOH . 
D 4 HOH A 97 597 4 HOH HOH . 
D 4 HOH A 98 598 63 HOH HOH . 
D 4 HOH A 99 599 45 HOH HOH . 
D 4 HOH A 100 600 23 HOH HOH . 
D 4 HOH A 101 601 93 HOH HOH . 
D 4 HOH A 102 602 23 HOH HOH . 
D 4 HOH A 103 603 89 HOH HOH . 
D 4 HOH A 104 604 18 HOH HOH . 
D 4 HOH A 105 605 94 HOH HOH . 
D 4 HOH A 106 606 31 HOH HOH . 
D 4 HOH A 107 607 117 HOH HOH . 
D 4 HOH A 108 608 47 HOH HOH . 
D 4 HOH A 109 609 71 HOH HOH . 
D 4 HOH A 110 610 40 HOH HOH . 
D 4 HOH A 111 611 113 HOH HOH . 
D 4 HOH A 112 612 65 HOH HOH . 
D 4 HOH A 113 613 95 HOH HOH . 
D 4 HOH A 114 614 112 HOH HOH . 
D 4 HOH A 115 615 27 HOH HOH . 
D 4 HOH A 116 616 82 HOH HOH . 
D 4 HOH A 117 617 26 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 53.704 36.395 60.352 1 63.9 ? N1 PLP 401 A 1 
HETATM 2 C C2 PLP . . . B 2 52.912 37.059 59.497 1 71.85 ? C2 PLP 401 A 1 
HETATM 3 C C2A PLP . . . B 2 53.329 37.189 58.068 1 63.47 ? C2A PLP 401 A 1 
HETATM 4 C C3 PLP . . . B 2 51.735 37.66 59.956 1 58.78 ? C3 PLP 401 A 1 
HETATM 5 O O3 PLP . . . B 2 50.999 38.353 59.064 1 72.56 ? O3 PLP 401 A 1 
HETATM 6 C C4 PLP . . . B 2 51.345 37.496 61.309 1 72.72 ? C4 PLP 401 A 1 
HETATM 7 C C4A PLP . . . B 2 50.099 38.105 61.793 1 69.33 ? C4A PLP 401 A 1 
HETATM 8 C C5 PLP . . . B 2 52.195 36.779 62.187 1 73.38 ? C5 PLP 401 A 1 
HETATM 9 C C6 PLP . . . B 2 53.353 36.271 61.647 1 68.6 ? C6 PLP 401 A 1 
HETATM 10 C C5A PLP . . . B 2 51.893 36.576 63.662 1 63.33 ? C5A PLP 401 A 1 
HETATM 11 O O4P PLP . . . B 2 51.504 37.787 64.412 1 65.17 ? O4P PLP 401 A 1 
HETATM 12 P P PLP . . . B 2 50.372 37.745 65.648 1 61.21 ? P PLP 401 A 1 
HETATM 13 O O1P PLP . . . B 2 49.125 37.153 64.992 1 58.5 ? O1P PLP 401 A 1 
HETATM 14 O O2P PLP . . . B 2 50.964 36.836 66.743 1 49.17 ? O2P PLP 401 A 1 
HETATM 15 O O3P PLP . . . B 2 50.22 39.226 66.143 1 45.39 ? O3P PLP 401 A 1 
#
_model_server_stats.io_time_ms              65 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           293 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           15 
#