data_2NMP
#
_model_server_result.job_id            -0ogq5LgB7-dNPyHvimgAg 
_model_server_result.datetime_utc      '2024-11-04 22:47:09' 
_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          2nmp 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":500}' 
#
_entry.id    2NMP 
#
_exptl.entry_id    2NMP 
_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    3 
_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            2NMP 
_cell.length_a            105.78 
_cell.length_b            107.57 
_cell.length_c            153.31 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2NMP 
_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 
_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 E N N 
? 2 F N N 
? 2 G 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 213 A LYS 212 1_555 E C4A PLP . A PLP 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.96 ? 
covale ? covale2 C NZ LYS 213 C LYS 212 1_555 F C4A PLP . C PLP 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? 
covale ? covale3 D NZ LYS 213 D LYS 212 1_555 G C4A PLP . D PLP 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? 
#
_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                     2NMP 
_atom_sites.fract_transf_matrix[1][1]    0.009454 
_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]    0.009296 
_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]    0.006523 
_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 2 PLP A 1 500 500 PLP PLP . 
F 2 PLP C 1 500 500 PLP PLP . 
G 2 PLP D 1 500 500 PLP PLP . 
H 3 HOH A 1 501 3 HOH HOH . 
H 3 HOH A 2 502 4 HOH HOH . 
H 3 HOH A 3 503 5 HOH HOH . 
H 3 HOH A 4 504 7 HOH HOH . 
H 3 HOH A 5 505 9 HOH HOH . 
H 3 HOH A 6 506 10 HOH HOH . 
H 3 HOH A 7 507 24 HOH HOH . 
H 3 HOH A 8 508 25 HOH HOH . 
H 3 HOH A 9 509 28 HOH HOH . 
H 3 HOH A 10 510 29 HOH HOH . 
H 3 HOH A 11 511 30 HOH HOH . 
H 3 HOH A 12 512 33 HOH HOH . 
H 3 HOH A 13 513 37 HOH HOH . 
H 3 HOH A 14 514 39 HOH HOH . 
H 3 HOH A 15 515 42 HOH HOH . 
H 3 HOH A 16 516 43 HOH HOH . 
H 3 HOH A 17 517 48 HOH HOH . 
H 3 HOH A 18 518 51 HOH HOH . 
H 3 HOH A 19 519 58 HOH HOH . 
H 3 HOH A 20 520 61 HOH HOH . 
H 3 HOH A 21 521 62 HOH HOH . 
H 3 HOH A 22 522 65 HOH HOH . 
H 3 HOH A 23 523 69 HOH HOH . 
H 3 HOH A 24 524 70 HOH HOH . 
H 3 HOH A 25 525 80 HOH HOH . 
H 3 HOH A 26 526 85 HOH HOH . 
H 3 HOH A 27 527 89 HOH HOH . 
H 3 HOH A 28 528 92 HOH HOH . 
H 3 HOH A 29 529 93 HOH HOH . 
H 3 HOH A 30 530 94 HOH HOH . 
H 3 HOH A 31 531 100 HOH HOH . 
H 3 HOH A 32 532 108 HOH HOH . 
H 3 HOH A 33 533 112 HOH HOH . 
H 3 HOH A 34 534 119 HOH HOH . 
H 3 HOH A 35 535 121 HOH HOH . 
H 3 HOH A 36 536 123 HOH HOH . 
H 3 HOH A 37 537 126 HOH HOH . 
H 3 HOH A 38 538 136 HOH HOH . 
H 3 HOH A 39 539 139 HOH HOH . 
H 3 HOH A 40 540 140 HOH HOH . 
H 3 HOH A 41 541 141 HOH HOH . 
H 3 HOH A 42 542 147 HOH HOH . 
I 3 HOH B 1 403 2 HOH HOH . 
I 3 HOH B 2 404 11 HOH HOH . 
I 3 HOH B 3 405 13 HOH HOH . 
I 3 HOH B 4 406 17 HOH HOH . 
I 3 HOH B 5 407 18 HOH HOH . 
I 3 HOH B 6 408 21 HOH HOH . 
I 3 HOH B 7 409 40 HOH HOH . 
I 3 HOH B 8 410 55 HOH HOH . 
I 3 HOH B 9 411 66 HOH HOH . 
I 3 HOH B 10 412 67 HOH HOH . 
I 3 HOH B 11 413 73 HOH HOH . 
I 3 HOH B 12 414 77 HOH HOH . 
I 3 HOH B 13 415 84 HOH HOH . 
I 3 HOH B 14 416 88 HOH HOH . 
I 3 HOH B 15 417 91 HOH HOH . 
I 3 HOH B 16 418 95 HOH HOH . 
I 3 HOH B 17 419 101 HOH HOH . 
I 3 HOH B 18 420 106 HOH HOH . 
I 3 HOH B 19 421 113 HOH HOH . 
I 3 HOH B 20 422 118 HOH HOH . 
I 3 HOH B 21 423 120 HOH HOH . 
I 3 HOH B 22 424 122 HOH HOH . 
I 3 HOH B 23 425 131 HOH HOH . 
I 3 HOH B 24 426 137 HOH HOH . 
I 3 HOH B 25 427 143 HOH HOH . 
I 3 HOH B 26 428 145 HOH HOH . 
I 3 HOH B 27 429 151 HOH HOH . 
I 3 HOH B 28 430 156 HOH HOH . 
J 3 HOH C 1 501 1 HOH HOH . 
J 3 HOH C 2 502 6 HOH HOH . 
J 3 HOH C 3 503 8 HOH HOH . 
J 3 HOH C 4 504 15 HOH HOH . 
J 3 HOH C 5 505 20 HOH HOH . 
J 3 HOH C 6 506 22 HOH HOH . 
J 3 HOH C 7 507 26 HOH HOH . 
J 3 HOH C 8 508 31 HOH HOH . 
J 3 HOH C 9 509 34 HOH HOH . 
J 3 HOH C 10 510 45 HOH HOH . 
J 3 HOH C 11 511 50 HOH HOH . 
J 3 HOH C 12 512 52 HOH HOH . 
J 3 HOH C 13 513 57 HOH HOH . 
J 3 HOH C 14 514 60 HOH HOH . 
J 3 HOH C 15 515 64 HOH HOH . 
J 3 HOH C 16 516 72 HOH HOH . 
J 3 HOH C 17 517 75 HOH HOH . 
J 3 HOH C 18 518 76 HOH HOH . 
J 3 HOH C 19 519 81 HOH HOH . 
J 3 HOH C 20 520 82 HOH HOH . 
J 3 HOH C 21 521 86 HOH HOH . 
J 3 HOH C 22 522 90 HOH HOH . 
J 3 HOH C 23 523 102 HOH HOH . 
J 3 HOH C 24 524 103 HOH HOH . 
J 3 HOH C 25 525 104 HOH HOH . 
J 3 HOH C 26 526 107 HOH HOH . 
J 3 HOH C 27 527 111 HOH HOH . 
J 3 HOH C 28 528 116 HOH HOH . 
J 3 HOH C 29 529 124 HOH HOH . 
J 3 HOH C 30 530 125 HOH HOH . 
J 3 HOH C 31 531 127 HOH HOH . 
J 3 HOH C 32 532 129 HOH HOH . 
J 3 HOH C 33 533 130 HOH HOH . 
J 3 HOH C 34 534 132 HOH HOH . 
J 3 HOH C 35 535 134 HOH HOH . 
J 3 HOH C 36 536 142 HOH HOH . 
J 3 HOH C 37 537 144 HOH HOH . 
J 3 HOH C 38 538 146 HOH HOH . 
J 3 HOH C 39 539 148 HOH HOH . 
J 3 HOH C 40 540 153 HOH HOH . 
J 3 HOH C 41 541 155 HOH HOH . 
J 3 HOH C 42 542 157 HOH HOH . 
K 3 HOH D 1 501 12 HOH HOH . 
K 3 HOH D 2 502 14 HOH HOH . 
K 3 HOH D 3 503 16 HOH HOH . 
K 3 HOH D 4 504 19 HOH HOH . 
K 3 HOH D 5 505 23 HOH HOH . 
K 3 HOH D 6 506 27 HOH HOH . 
K 3 HOH D 7 507 32 HOH HOH . 
K 3 HOH D 8 508 35 HOH HOH . 
K 3 HOH D 9 509 36 HOH HOH . 
K 3 HOH D 10 510 38 HOH HOH . 
K 3 HOH D 11 511 41 HOH HOH . 
K 3 HOH D 12 512 44 HOH HOH . 
K 3 HOH D 13 513 46 HOH HOH . 
K 3 HOH D 14 514 47 HOH HOH . 
K 3 HOH D 15 515 49 HOH HOH . 
K 3 HOH D 16 516 53 HOH HOH . 
K 3 HOH D 17 517 54 HOH HOH . 
K 3 HOH D 18 518 56 HOH HOH . 
K 3 HOH D 19 519 59 HOH HOH . 
K 3 HOH D 20 520 63 HOH HOH . 
K 3 HOH D 21 521 68 HOH HOH . 
K 3 HOH D 22 522 71 HOH HOH . 
K 3 HOH D 23 523 74 HOH HOH . 
K 3 HOH D 24 524 78 HOH HOH . 
K 3 HOH D 25 525 79 HOH HOH . 
K 3 HOH D 26 526 83 HOH HOH . 
K 3 HOH D 27 527 87 HOH HOH . 
K 3 HOH D 28 528 96 HOH HOH . 
K 3 HOH D 29 529 97 HOH HOH . 
K 3 HOH D 30 530 98 HOH HOH . 
K 3 HOH D 31 531 99 HOH HOH . 
K 3 HOH D 32 532 105 HOH HOH . 
K 3 HOH D 33 533 109 HOH HOH . 
K 3 HOH D 34 534 110 HOH HOH . 
K 3 HOH D 35 535 114 HOH HOH . 
K 3 HOH D 36 536 115 HOH HOH . 
K 3 HOH D 37 537 117 HOH HOH . 
K 3 HOH D 38 538 128 HOH HOH . 
K 3 HOH D 39 539 133 HOH HOH . 
K 3 HOH D 40 540 135 HOH HOH . 
K 3 HOH D 41 541 138 HOH HOH . 
K 3 HOH D 42 542 149 HOH HOH . 
K 3 HOH D 43 543 150 HOH HOH . 
K 3 HOH D 44 544 152 HOH HOH . 
K 3 HOH D 45 545 154 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 2 -18.94 35.42 -16.943 1 25.78 ? N1 PLP 500 A 1 
HETATM 2 C C2 PLP . . . E 2 -18.993 36.546 -17.7 1 27.73 ? C2 PLP 500 A 1 
HETATM 3 C C2A PLP . . . E 2 -17.909 37.679 -17.604 1 27.32 ? C2A PLP 500 A 1 
HETATM 4 C C3 PLP . . . E 2 -20.037 36.712 -18.608 1 26.78 ? C3 PLP 500 A 1 
HETATM 5 O O3 PLP . . . E 2 -20.071 37.837 -19.362 1 27.09 ? O3 PLP 500 A 1 
HETATM 6 C C4 PLP . . . E 2 -21.024 35.738 -18.728 1 27.44 ? C4 PLP 500 A 1 
HETATM 7 C C4A PLP . . . E 2 -22.161 35.963 -19.717 1 26.74 ? C4A PLP 500 A 1 
HETATM 8 C C5 PLP . . . E 2 -20.967 34.583 -17.929 1 27.34 ? C5 PLP 500 A 1 
HETATM 9 C C6 PLP . . . E 2 -19.881 34.48 -17.037 1 27.38 ? C6 PLP 500 A 1 
HETATM 10 C C5A PLP . . . E 2 -22.009 33.449 -17.934 1 26.78 ? C5A PLP 500 A 1 
HETATM 11 O O4P PLP . . . E 2 -21.901 32.602 -19.059 1 29.57 ? O4P PLP 500 A 1 
HETATM 12 P P PLP . . . E 2 -23.156 32.041 -19.94 1 29.6 ? P PLP 500 A 1 
HETATM 13 O O1P PLP . . . E 2 -22.597 31.378 -21.145 1 25.52 ? O1P PLP 500 A 1 
HETATM 14 O O2P PLP . . . E 2 -24.137 33.334 -20.184 1 27.94 ? O2P PLP 500 A 1 
HETATM 15 O O3P PLP . . . E 2 -23.993 31.084 -18.978 1 28.15 ? O3P PLP 500 A 1 
#
_model_server_stats.io_time_ms              72 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           271 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           15 
#