data_3LVJ
#
_model_server_result.job_id            XbIp-6ntL8wA7z_E9AxeZw 
_model_server_result.datetime_utc      '2024-12-02 19:12:06' 
_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          3lvj 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":764}' 
#
_entry.id    3LVJ 
#
_exptl.entry_id    3LVJ 
_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            3LVJ 
_cell.length_a            72.299 
_cell.length_b            106.545 
_cell.length_c            122.106 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3LVJ 
_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 
_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 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 225 A LYS 206 1_555 E C4A PLP . A PLP 764 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.605 ? 
covale ? covale2 B NZ LYS 225 B LYS 206 1_555 F C4A PLP . B PLP 764 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.624 ? 
#
_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                     3LVJ 
_atom_sites.fract_transf_matrix[1][1]    0.013831 
_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]    0.009386 
_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]    0.00819 
_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 1 764 764 PLP PLP . 
F 3 PLP B 1 764 764 PLP PLP . 
G 4 HOH A 1 405 2 HOH HOH . 
G 4 HOH A 2 406 3 HOH HOH . 
G 4 HOH A 3 407 7 HOH HOH . 
G 4 HOH A 4 408 9 HOH HOH . 
G 4 HOH A 5 409 11 HOH HOH . 
G 4 HOH A 6 410 12 HOH HOH . 
G 4 HOH A 7 411 16 HOH HOH . 
G 4 HOH A 8 412 18 HOH HOH . 
G 4 HOH A 9 413 19 HOH HOH . 
G 4 HOH A 10 414 25 HOH HOH . 
G 4 HOH A 11 415 26 HOH HOH . 
G 4 HOH A 12 416 27 HOH HOH . 
G 4 HOH A 13 417 30 HOH HOH . 
G 4 HOH A 14 418 31 HOH HOH . 
G 4 HOH A 15 419 32 HOH HOH . 
G 4 HOH A 16 420 34 HOH HOH . 
G 4 HOH A 17 421 35 HOH HOH . 
G 4 HOH A 18 422 36 HOH HOH . 
G 4 HOH A 19 423 37 HOH HOH . 
G 4 HOH A 20 424 40 HOH HOH . 
G 4 HOH A 21 425 43 HOH HOH . 
G 4 HOH A 22 426 44 HOH HOH . 
G 4 HOH A 23 427 45 HOH HOH . 
G 4 HOH A 24 428 47 HOH HOH . 
G 4 HOH A 25 429 50 HOH HOH . 
G 4 HOH A 26 430 51 HOH HOH . 
G 4 HOH A 27 431 55 HOH HOH . 
G 4 HOH A 28 432 59 HOH HOH . 
G 4 HOH A 29 433 60 HOH HOH . 
G 4 HOH A 30 434 61 HOH HOH . 
G 4 HOH A 31 435 62 HOH HOH . 
G 4 HOH A 32 436 63 HOH HOH . 
G 4 HOH A 33 437 64 HOH HOH . 
G 4 HOH A 34 438 66 HOH HOH . 
G 4 HOH A 35 439 68 HOH HOH . 
G 4 HOH A 36 440 69 HOH HOH . 
G 4 HOH A 37 441 70 HOH HOH . 
G 4 HOH A 38 442 71 HOH HOH . 
G 4 HOH A 39 443 73 HOH HOH . 
G 4 HOH A 40 444 75 HOH HOH . 
G 4 HOH A 41 445 76 HOH HOH . 
G 4 HOH A 42 446 79 HOH HOH . 
G 4 HOH A 43 447 81 HOH HOH . 
G 4 HOH A 44 448 89 HOH HOH . 
G 4 HOH A 45 449 90 HOH HOH . 
G 4 HOH A 46 450 92 HOH HOH . 
G 4 HOH A 47 451 93 HOH HOH . 
G 4 HOH A 48 452 97 HOH HOH . 
G 4 HOH A 49 453 98 HOH HOH . 
G 4 HOH A 50 454 100 HOH HOH . 
G 4 HOH A 51 455 101 HOH HOH . 
G 4 HOH A 52 456 102 HOH HOH . 
G 4 HOH A 53 457 104 HOH HOH . 
G 4 HOH A 54 458 105 HOH HOH . 
G 4 HOH A 55 459 106 HOH HOH . 
G 4 HOH A 56 460 109 HOH HOH . 
G 4 HOH A 57 461 110 HOH HOH . 
G 4 HOH A 58 462 111 HOH HOH . 
G 4 HOH A 59 463 112 HOH HOH . 
G 4 HOH A 60 464 115 HOH HOH . 
G 4 HOH A 61 465 117 HOH HOH . 
G 4 HOH A 62 466 118 HOH HOH . 
G 4 HOH A 63 467 119 HOH HOH . 
G 4 HOH A 64 468 120 HOH HOH . 
G 4 HOH A 65 469 121 HOH HOH . 
G 4 HOH A 66 470 123 HOH HOH . 
G 4 HOH A 67 471 126 HOH HOH . 
G 4 HOH A 68 472 128 HOH HOH . 
G 4 HOH A 69 473 129 HOH HOH . 
G 4 HOH A 70 474 130 HOH HOH . 
G 4 HOH A 71 475 131 HOH HOH . 
G 4 HOH A 72 476 134 HOH HOH . 
G 4 HOH A 73 477 135 HOH HOH . 
G 4 HOH A 74 478 137 HOH HOH . 
G 4 HOH A 75 479 138 HOH HOH . 
G 4 HOH A 76 480 140 HOH HOH . 
G 4 HOH A 77 481 152 HOH HOH . 
G 4 HOH A 78 482 154 HOH HOH . 
G 4 HOH A 79 483 157 HOH HOH . 
G 4 HOH A 80 484 160 HOH HOH . 
G 4 HOH A 81 485 162 HOH HOH . 
G 4 HOH A 82 486 170 HOH HOH . 
G 4 HOH A 83 487 173 HOH HOH . 
G 4 HOH A 84 488 175 HOH HOH . 
G 4 HOH A 85 489 181 HOH HOH . 
G 4 HOH A 86 490 184 HOH HOH . 
G 4 HOH A 87 491 186 HOH HOH . 
G 4 HOH A 88 492 192 HOH HOH . 
G 4 HOH A 89 493 193 HOH HOH . 
G 4 HOH A 90 494 196 HOH HOH . 
G 4 HOH A 91 495 199 HOH HOH . 
G 4 HOH A 92 496 200 HOH HOH . 
G 4 HOH A 93 497 205 HOH HOH . 
G 4 HOH A 94 498 209 HOH HOH . 
G 4 HOH A 95 499 210 HOH HOH . 
G 4 HOH A 96 500 211 HOH HOH . 
G 4 HOH A 97 501 136 HOH HOH . 
H 4 HOH B 1 405 1 HOH HOH . 
H 4 HOH B 2 406 4 HOH HOH . 
H 4 HOH B 3 407 5 HOH HOH . 
H 4 HOH B 4 408 6 HOH HOH . 
H 4 HOH B 5 409 10 HOH HOH . 
H 4 HOH B 6 410 13 HOH HOH . 
H 4 HOH B 7 411 14 HOH HOH . 
H 4 HOH B 8 412 15 HOH HOH . 
H 4 HOH B 9 413 17 HOH HOH . 
H 4 HOH B 10 414 20 HOH HOH . 
H 4 HOH B 11 415 21 HOH HOH . 
H 4 HOH B 12 416 22 HOH HOH . 
H 4 HOH B 13 417 23 HOH HOH . 
H 4 HOH B 14 418 24 HOH HOH . 
H 4 HOH B 15 419 28 HOH HOH . 
H 4 HOH B 16 420 29 HOH HOH . 
H 4 HOH B 17 421 33 HOH HOH . 
H 4 HOH B 18 422 39 HOH HOH . 
H 4 HOH B 19 423 41 HOH HOH . 
H 4 HOH B 20 424 42 HOH HOH . 
H 4 HOH B 21 425 46 HOH HOH . 
H 4 HOH B 22 426 48 HOH HOH . 
H 4 HOH B 23 427 49 HOH HOH . 
H 4 HOH B 24 428 52 HOH HOH . 
H 4 HOH B 25 429 53 HOH HOH . 
H 4 HOH B 26 430 54 HOH HOH . 
H 4 HOH B 27 431 56 HOH HOH . 
H 4 HOH B 28 432 57 HOH HOH . 
H 4 HOH B 29 433 58 HOH HOH . 
H 4 HOH B 30 434 65 HOH HOH . 
H 4 HOH B 31 435 67 HOH HOH . 
H 4 HOH B 32 436 72 HOH HOH . 
H 4 HOH B 33 437 74 HOH HOH . 
H 4 HOH B 34 438 77 HOH HOH . 
H 4 HOH B 35 439 78 HOH HOH . 
H 4 HOH B 36 440 80 HOH HOH . 
H 4 HOH B 37 441 82 HOH HOH . 
H 4 HOH B 38 442 83 HOH HOH . 
H 4 HOH B 39 443 84 HOH HOH . 
H 4 HOH B 40 444 85 HOH HOH . 
H 4 HOH B 41 445 88 HOH HOH . 
H 4 HOH B 42 446 91 HOH HOH . 
H 4 HOH B 43 447 94 HOH HOH . 
H 4 HOH B 44 448 95 HOH HOH . 
H 4 HOH B 45 449 96 HOH HOH . 
H 4 HOH B 46 450 99 HOH HOH . 
H 4 HOH B 47 451 103 HOH HOH . 
H 4 HOH B 48 452 107 HOH HOH . 
H 4 HOH B 49 453 108 HOH HOH . 
H 4 HOH B 50 454 113 HOH HOH . 
H 4 HOH B 51 455 114 HOH HOH . 
H 4 HOH B 52 456 116 HOH HOH . 
H 4 HOH B 53 457 122 HOH HOH . 
H 4 HOH B 54 458 124 HOH HOH . 
H 4 HOH B 55 459 133 HOH HOH . 
H 4 HOH B 56 461 142 HOH HOH . 
H 4 HOH B 57 462 143 HOH HOH . 
H 4 HOH B 58 463 145 HOH HOH . 
H 4 HOH B 59 464 148 HOH HOH . 
H 4 HOH B 60 465 149 HOH HOH . 
H 4 HOH B 61 466 150 HOH HOH . 
H 4 HOH B 62 467 151 HOH HOH . 
H 4 HOH B 63 468 153 HOH HOH . 
H 4 HOH B 64 469 156 HOH HOH . 
H 4 HOH B 65 470 158 HOH HOH . 
H 4 HOH B 66 471 159 HOH HOH . 
H 4 HOH B 67 472 161 HOH HOH . 
H 4 HOH B 68 473 163 HOH HOH . 
H 4 HOH B 69 474 164 HOH HOH . 
H 4 HOH B 70 475 166 HOH HOH . 
H 4 HOH B 71 476 168 HOH HOH . 
H 4 HOH B 72 477 169 HOH HOH . 
H 4 HOH B 73 478 172 HOH HOH . 
H 4 HOH B 74 479 174 HOH HOH . 
H 4 HOH B 75 480 176 HOH HOH . 
H 4 HOH B 76 481 177 HOH HOH . 
H 4 HOH B 77 482 178 HOH HOH . 
H 4 HOH B 78 483 179 HOH HOH . 
H 4 HOH B 79 484 180 HOH HOH . 
H 4 HOH B 80 485 182 HOH HOH . 
H 4 HOH B 81 486 185 HOH HOH . 
H 4 HOH B 82 487 187 HOH HOH . 
H 4 HOH B 83 488 188 HOH HOH . 
H 4 HOH B 84 489 189 HOH HOH . 
H 4 HOH B 85 490 191 HOH HOH . 
H 4 HOH B 86 491 194 HOH HOH . 
H 4 HOH B 87 492 195 HOH HOH . 
H 4 HOH B 88 493 197 HOH HOH . 
H 4 HOH B 89 494 201 HOH HOH . 
H 4 HOH B 90 495 202 HOH HOH . 
H 4 HOH B 91 496 203 HOH HOH . 
H 4 HOH B 92 497 204 HOH HOH . 
H 4 HOH B 93 498 207 HOH HOH . 
H 4 HOH B 94 499 208 HOH HOH . 
H 4 HOH B 95 500 213 HOH HOH . 
I 4 HOH C 1 82 38 HOH HOH . 
I 4 HOH C 2 86 86 HOH HOH . 
I 4 HOH C 3 125 125 HOH HOH . 
I 4 HOH C 4 132 132 HOH HOH . 
I 4 HOH C 5 141 141 HOH HOH . 
I 4 HOH C 6 146 146 HOH HOH . 
I 4 HOH C 7 165 165 HOH HOH . 
I 4 HOH C 8 171 171 HOH HOH . 
I 4 HOH C 9 183 183 HOH HOH . 
I 4 HOH C 10 190 190 HOH HOH . 
I 4 HOH C 11 206 206 HOH HOH . 
J 4 HOH D 1 82 8 HOH HOH . 
J 4 HOH D 2 87 87 HOH HOH . 
J 4 HOH D 3 127 127 HOH HOH . 
J 4 HOH D 4 139 139 HOH HOH . 
J 4 HOH D 5 144 144 HOH HOH . 
J 4 HOH D 6 147 147 HOH HOH . 
J 4 HOH D 7 155 155 HOH HOH . 
J 4 HOH D 8 167 167 HOH HOH . 
J 4 HOH D 9 198 198 HOH HOH . 
J 4 HOH D 10 212 212 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 -10.797 -4.041 -8.068 1 69.06 ? N1 PLP 764 A 1 
HETATM 2 C C2 PLP . . . E 3 -11.695 -4.539 -8.949 1 69.06 ? C2 PLP 764 A 1 
HETATM 3 C C2A PLP . . . E 3 -13.156 -4.47 -8.658 1 69.06 ? C2A PLP 764 A 1 
HETATM 4 C C3 PLP . . . E 3 -11.25 -5.115 -10.133 1 69.06 ? C3 PLP 764 A 1 
HETATM 5 O O3 PLP . . . E 3 -12.173 -5.633 -11.055 1 69.06 ? O3 PLP 764 A 1 
HETATM 6 C C4 PLP . . . E 3 -9.897 -5.184 -10.419 1 69.06 ? C4 PLP 764 A 1 
HETATM 7 C C4A PLP . . . E 3 -9.446 -5.818 -11.733 1 69.06 ? C4A PLP 764 A 1 
HETATM 8 C C5 PLP . . . E 3 -8.987 -4.67 -9.497 1 69.06 ? C5 PLP 764 A 1 
HETATM 9 C C6 PLP . . . E 3 -9.478 -4.095 -8.316 1 69.06 ? C6 PLP 764 A 1 
HETATM 10 C C5A PLP . . . E 3 -7.495 -4.728 -9.785 1 69.06 ? C5A PLP 764 A 1 
HETATM 11 O O4P PLP . . . E 3 -6.989 -3.799 -10.838 1 69.06 ? O4P PLP 764 A 1 
HETATM 12 P P PLP . . . E 3 -5.536 -3.934 -11.365 1 69.06 ? P PLP 764 A 1 
HETATM 13 O O1P PLP . . . E 3 -5.139 -2.678 -12.066 1 69.06 ? O1P PLP 764 A 1 
HETATM 14 O O2P PLP . . . E 3 -5.452 -5.087 -12.313 1 69.06 ? O2P PLP 764 A 1 
HETATM 15 O O3P PLP . . . E 3 -4.574 -4.193 -10.169 1 69.06 ? O3P PLP 764 A 1 
#
_model_server_stats.io_time_ms              31 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           308 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           15 
#