data_4EB5
#
_model_server_result.job_id            QkmaLRKdSllAQJD1K0ICqg 
_model_server_result.datetime_utc      '2024-10-19 04:33:33' 
_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          4eb5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":401}' 
#
_entry.id    4EB5 
#
_exptl.entry_id    4EB5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              247.142 
_entity.id                          3 
_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            4EB5 
_cell.length_a            76.411 
_cell.length_b            94.897 
_cell.length_c            150.585 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4EB5 
_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    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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,N,O,P 
_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
? 3 E N N 
? 3 I 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
metalc ? metalc1 A SG CYS 321 A CYS 321 1_555 K FE2 FES . C FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.401 ? 
metalc ? metalc2 B SG CYS 321 B CYS 321 1_555 L FE2 FES . D FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.519 ? 
metalc ? metalc3 C SG CYS 33 C CYS 33 1_555 K FE2 FES . C FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? 
metalc ? metalc4 C SG CYS 58 C CYS 58 1_555 K FE1 FES . C FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? 
metalc ? metalc5 C SG CYS 102 C CYS 102 1_555 K FE1 FES . C FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? 
metalc ? metalc6 D SG CYS 33 D CYS 33 1_555 L FE2 FES . D FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? 
metalc ? metalc7 D SG CYS 58 D CYS 58 1_555 L FE1 FES . D FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? 
metalc ? metalc8 D SG CYS 102 D CYS 102 1_555 L FE1 FES . D FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? 
#
_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 310 n y 
N1 C6 PLP sing 311 n y 
C2 C2A PLP sing 312 n n 
C2 C3 PLP sing 313 n y 
C2A H2A1 PLP sing 314 n n 
C2A H2A2 PLP sing 315 n n 
C2A H2A3 PLP sing 316 n n 
C3 O3 PLP sing 317 n n 
C3 C4 PLP doub 318 n y 
O3 HO3 PLP sing 319 n n 
C4 C4A PLP sing 320 n n 
C4 C5 PLP sing 321 n y 
C4A O4A PLP doub 322 n n 
C4A H4A PLP sing 323 n n 
C5 C6 PLP doub 324 n y 
C5 C5A PLP sing 325 n n 
C6 H6 PLP sing 326 n n 
C5A O4P PLP sing 327 n n 
C5A H5A1 PLP sing 328 n n 
C5A H5A2 PLP sing 329 n n 
O4P P PLP sing 330 n n 
P O1P PLP doub 331 n n 
P O2P PLP sing 332 n n 
P O3P PLP sing 333 n n 
O2P HOP2 PLP sing 334 n n 
O3P HOP3 PLP sing 335 n n 
#
_atom_sites.entry_id                     4EB5 
_atom_sites.fract_transf_matrix[1][1]    0.013087 
_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]    0.010538 
_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]    0.006641 
_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
E 3 PLP A 1 401 1 PLP PLP . 
F 4 GOL A 1 402 3 GOL GOL . 
G 4 GOL A 1 403 4 GOL GOL . 
H 5 EPE A 1 404 6 EPE EPE . 
I 3 PLP B 1 401 2 PLP PLP . 
J 4 GOL B 1 402 5 GOL GOL . 
K 6 FES C 1 201 7 FES FES . 
L 6 FES D 1 201 8 FES FES . 
M 7 HOH A 1 501 1 HOH HOH . 
M 7 HOH A 2 502 2 HOH HOH . 
M 7 HOH A 3 503 3 HOH HOH . 
M 7 HOH A 4 504 4 HOH HOH . 
M 7 HOH A 5 505 5 HOH HOH . 
M 7 HOH A 6 506 8 HOH HOH . 
M 7 HOH A 7 507 10 HOH HOH . 
M 7 HOH A 8 508 11 HOH HOH . 
M 7 HOH A 9 509 16 HOH HOH . 
M 7 HOH A 10 510 17 HOH HOH . 
M 7 HOH A 11 511 18 HOH HOH . 
M 7 HOH A 12 512 19 HOH HOH . 
M 7 HOH A 13 513 20 HOH HOH . 
M 7 HOH A 14 514 21 HOH HOH . 
M 7 HOH A 15 515 22 HOH HOH . 
M 7 HOH A 16 516 24 HOH HOH . 
M 7 HOH A 17 517 25 HOH HOH . 
M 7 HOH A 18 518 26 HOH HOH . 
M 7 HOH A 19 519 27 HOH HOH . 
M 7 HOH A 20 520 28 HOH HOH . 
M 7 HOH A 21 521 31 HOH HOH . 
M 7 HOH A 22 522 33 HOH HOH . 
M 7 HOH A 23 523 44 HOH HOH . 
M 7 HOH A 24 524 46 HOH HOH . 
M 7 HOH A 25 525 47 HOH HOH . 
M 7 HOH A 26 526 50 HOH HOH . 
M 7 HOH A 27 527 52 HOH HOH . 
M 7 HOH A 28 528 53 HOH HOH . 
M 7 HOH A 29 529 54 HOH HOH . 
M 7 HOH A 30 530 55 HOH HOH . 
M 7 HOH A 31 531 56 HOH HOH . 
M 7 HOH A 32 532 59 HOH HOH . 
M 7 HOH A 33 533 62 HOH HOH . 
M 7 HOH A 34 534 63 HOH HOH . 
M 7 HOH A 35 535 64 HOH HOH . 
M 7 HOH A 36 536 66 HOH HOH . 
M 7 HOH A 37 537 67 HOH HOH . 
M 7 HOH A 38 538 68 HOH HOH . 
M 7 HOH A 39 539 69 HOH HOH . 
M 7 HOH A 40 540 70 HOH HOH . 
M 7 HOH A 41 541 71 HOH HOH . 
M 7 HOH A 42 542 72 HOH HOH . 
M 7 HOH A 43 543 74 HOH HOH . 
M 7 HOH A 44 544 75 HOH HOH . 
M 7 HOH A 45 545 76 HOH HOH . 
M 7 HOH A 46 546 79 HOH HOH . 
M 7 HOH A 47 547 82 HOH HOH . 
M 7 HOH A 48 548 83 HOH HOH . 
M 7 HOH A 49 549 84 HOH HOH . 
M 7 HOH A 50 550 85 HOH HOH . 
M 7 HOH A 51 551 86 HOH HOH . 
M 7 HOH A 52 552 87 HOH HOH . 
M 7 HOH A 53 553 88 HOH HOH . 
M 7 HOH A 54 554 89 HOH HOH . 
M 7 HOH A 55 555 90 HOH HOH . 
M 7 HOH A 56 556 91 HOH HOH . 
M 7 HOH A 57 557 92 HOH HOH . 
M 7 HOH A 58 558 93 HOH HOH . 
M 7 HOH A 59 559 94 HOH HOH . 
M 7 HOH A 60 560 95 HOH HOH . 
M 7 HOH A 61 561 97 HOH HOH . 
M 7 HOH A 62 562 98 HOH HOH . 
M 7 HOH A 63 563 99 HOH HOH . 
M 7 HOH A 64 564 100 HOH HOH . 
M 7 HOH A 65 565 101 HOH HOH . 
M 7 HOH A 66 566 103 HOH HOH . 
M 7 HOH A 67 567 105 HOH HOH . 
M 7 HOH A 68 568 106 HOH HOH . 
M 7 HOH A 69 569 108 HOH HOH . 
M 7 HOH A 70 570 109 HOH HOH . 
M 7 HOH A 71 571 111 HOH HOH . 
M 7 HOH A 72 572 114 HOH HOH . 
M 7 HOH A 73 573 120 HOH HOH . 
M 7 HOH A 74 574 122 HOH HOH . 
M 7 HOH A 75 575 123 HOH HOH . 
M 7 HOH A 76 576 125 HOH HOH . 
M 7 HOH A 77 577 128 HOH HOH . 
M 7 HOH A 78 578 129 HOH HOH . 
M 7 HOH A 79 579 130 HOH HOH . 
M 7 HOH A 80 580 131 HOH HOH . 
M 7 HOH A 81 581 132 HOH HOH . 
M 7 HOH A 82 582 133 HOH HOH . 
M 7 HOH A 83 583 135 HOH HOH . 
M 7 HOH A 84 584 136 HOH HOH . 
M 7 HOH A 85 585 137 HOH HOH . 
M 7 HOH A 86 586 138 HOH HOH . 
M 7 HOH A 87 587 139 HOH HOH . 
M 7 HOH A 88 588 140 HOH HOH . 
M 7 HOH A 89 589 141 HOH HOH . 
M 7 HOH A 90 590 142 HOH HOH . 
M 7 HOH A 91 591 143 HOH HOH . 
M 7 HOH A 92 592 144 HOH HOH . 
M 7 HOH A 93 593 146 HOH HOH . 
M 7 HOH A 94 594 147 HOH HOH . 
M 7 HOH A 95 595 148 HOH HOH . 
M 7 HOH A 96 596 149 HOH HOH . 
M 7 HOH A 97 597 150 HOH HOH . 
M 7 HOH A 98 598 151 HOH HOH . 
M 7 HOH A 99 599 152 HOH HOH . 
M 7 HOH A 100 600 153 HOH HOH . 
M 7 HOH A 101 601 154 HOH HOH . 
M 7 HOH A 102 602 157 HOH HOH . 
N 7 HOH B 1 501 6 HOH HOH . 
N 7 HOH B 2 502 7 HOH HOH . 
N 7 HOH B 3 503 9 HOH HOH . 
N 7 HOH B 4 504 12 HOH HOH . 
N 7 HOH B 5 505 13 HOH HOH . 
N 7 HOH B 6 506 14 HOH HOH . 
N 7 HOH B 7 507 15 HOH HOH . 
N 7 HOH B 8 508 23 HOH HOH . 
N 7 HOH B 9 509 29 HOH HOH . 
N 7 HOH B 10 510 30 HOH HOH . 
N 7 HOH B 11 511 34 HOH HOH . 
N 7 HOH B 12 512 35 HOH HOH . 
N 7 HOH B 13 513 36 HOH HOH . 
N 7 HOH B 14 514 37 HOH HOH . 
N 7 HOH B 15 515 38 HOH HOH . 
N 7 HOH B 16 516 39 HOH HOH . 
N 7 HOH B 17 517 40 HOH HOH . 
N 7 HOH B 18 518 41 HOH HOH . 
N 7 HOH B 19 519 49 HOH HOH . 
N 7 HOH B 20 520 51 HOH HOH . 
N 7 HOH B 21 521 57 HOH HOH . 
N 7 HOH B 22 522 58 HOH HOH . 
N 7 HOH B 23 523 60 HOH HOH . 
N 7 HOH B 24 524 61 HOH HOH . 
N 7 HOH B 25 525 65 HOH HOH . 
N 7 HOH B 26 526 78 HOH HOH . 
N 7 HOH B 27 527 80 HOH HOH . 
N 7 HOH B 28 528 81 HOH HOH . 
N 7 HOH B 29 529 96 HOH HOH . 
N 7 HOH B 30 530 102 HOH HOH . 
N 7 HOH B 31 531 110 HOH HOH . 
N 7 HOH B 32 532 112 HOH HOH . 
N 7 HOH B 33 533 113 HOH HOH . 
N 7 HOH B 34 534 116 HOH HOH . 
N 7 HOH B 35 535 117 HOH HOH . 
N 7 HOH B 36 536 118 HOH HOH . 
N 7 HOH B 37 537 119 HOH HOH . 
N 7 HOH B 38 538 121 HOH HOH . 
N 7 HOH B 39 539 126 HOH HOH . 
N 7 HOH B 40 540 127 HOH HOH . 
N 7 HOH B 41 541 134 HOH HOH . 
N 7 HOH B 42 542 145 HOH HOH . 
N 7 HOH B 43 543 155 HOH HOH . 
N 7 HOH B 44 544 156 HOH HOH . 
N 7 HOH B 45 545 158 HOH HOH . 
N 7 HOH B 46 546 159 HOH HOH . 
N 7 HOH B 47 547 160 HOH HOH . 
N 7 HOH B 48 548 161 HOH HOH . 
N 7 HOH B 49 549 162 HOH HOH . 
N 7 HOH B 50 550 163 HOH HOH . 
N 7 HOH B 51 551 164 HOH HOH . 
O 7 HOH C 1 301 42 HOH HOH . 
O 7 HOH C 2 302 43 HOH HOH . 
O 7 HOH C 3 303 45 HOH HOH . 
O 7 HOH C 4 304 73 HOH HOH . 
O 7 HOH C 5 305 115 HOH HOH . 
O 7 HOH C 6 306 166 HOH HOH . 
O 7 HOH C 7 307 167 HOH HOH . 
O 7 HOH C 8 308 168 HOH HOH . 
P 7 HOH D 1 301 77 HOH HOH . 
P 7 HOH D 2 302 124 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 . . . E 3 -2.366 12.287 -1.999 0.9 25.8 ? N1 PLP 401 A 1 
HETATM 2 C C2 PLP . . . E 3 -2.397 11.239 -1.14 0.9 28.45 ? C2 PLP 401 A 1 
HETATM 3 C C2A PLP . . . E 3 -2.863 11.473 0.287 0.9 28.61 ? C2A PLP 401 A 1 
HETATM 4 C C3 PLP . . . E 3 -2.029 9.955 -1.594 0.9 28.2 ? C3 PLP 401 A 1 
HETATM 5 O O3 PLP . . . E 3 -2.06 8.887 -0.749 0.9 23.91 ? O3 PLP 401 A 1 
HETATM 6 C C4 PLP . . . E 3 -1.634 9.794 -2.916 0.9 28.59 ? C4 PLP 401 A 1 
HETATM 7 C C4A PLP . . . E 3 -1.23 8.466 -3.393 0.9 30.67 ? C4A PLP 401 A 1 
HETATM 8 O O4A PLP . . . E 3 -1.972 7.528 -3.221 0.9 36.08 ? O4A PLP 401 A 1 
HETATM 9 C C5 PLP . . . E 3 -1.603 10.902 -3.768 0.9 30.23 ? C5 PLP 401 A 1 
HETATM 10 C C6 PLP . . . E 3 -1.985 12.148 -3.278 0.9 27.63 ? C6 PLP 401 A 1 
HETATM 11 C C5A PLP . . . E 3 -1.207 10.807 -5.236 0.9 32.53 ? C5A PLP 401 A 1 
HETATM 12 O O4P PLP . . . E 3 -2.208 10.103 -6.014 0.9 32.4 ? O4P PLP 401 A 1 
HETATM 13 P P PLP . . . E 3 -1.866 9.512 -7.477 0.9 33.14 ? P PLP 401 A 1 
HETATM 14 O O1P PLP . . . E 3 -1.761 10.754 -8.323 0.9 34.98 ? O1P PLP 401 A 1 
HETATM 15 O O2P PLP . . . E 3 -3.008 8.664 -7.915 0.9 30.74 ? O2P PLP 401 A 1 
HETATM 16 O O3P PLP . . . E 3 -0.539 8.791 -7.363 0.9 32.57 ? O3P PLP 401 A 1 
#
_model_server_stats.io_time_ms              116 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           356 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           16 
#