data_1M54
#
_model_server_result.job_id            6oxNg0679wvl279EcJVR9A 
_model_server_result.datetime_utc      '2024-11-24 04:31:38' 
_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          1m54 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":1110}' 
#
_entry.id    1M54 
#
_exptl.entry_id    1M54 
_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    6 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         102.01 
_cell.angle_beta          101.53 
_cell.angle_gamma         112.6 
_cell.entry_id            1M54 
_cell.length_a            85.74 
_cell.length_b            85.626 
_cell.length_c            97.082 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1M54 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,G,H,I,J,S,T 1 1 
C,D,K,L,M,N,U,V 2 1 
E,F,O,P,Q,R,W,X 3 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 G N N 
? 2 I N N 
? 2 K N N 
? 2 M N N 
? 2 O N N 
? 2 Q 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 76 A LYS 119 1_555 G C4A PLP . A PLP 1110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? 
covale ? covale2 B NZ LYS 76 B LYS 119 1_555 I C4A PLP . B PLP 1210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.025 ? 
covale ? covale3 C NZ LYS 76 C LYS 119 1_555 K C4A PLP . C PLP 1310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.05 ? 
covale ? covale4 D NZ LYS 76 D LYS 119 1_555 M C4A PLP . D PLP 1410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.471 ? 
covale ? covale5 E NZ LYS 76 E LYS 119 1_555 O C4A PLP . E PLP 1510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? 
covale ? covale6 F NZ LYS 76 F LYS 119 1_555 Q C4A PLP . F PLP 1610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.474 ? 
metalc ? metalc1 A SG CYS 9 A CYS 52 1_555 H FE HEM . A HEM 1120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? 
metalc ? metalc2 A NE2 HIS 22 A HIS 65 1_555 H FE HEM . A HEM 1120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? 
metalc ? metalc3 B SG CYS 9 B CYS 52 1_555 J FE HEM . B HEM 1220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? 
metalc ? metalc4 B NE2 HIS 22 B HIS 65 1_555 J FE HEM . B HEM 1220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? 
metalc ? metalc5 C SG CYS 9 C CYS 52 1_555 L FE HEM . C HEM 1320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? 
metalc ? metalc6 C NE2 HIS 22 C HIS 65 1_555 L FE HEM . C HEM 1320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? 
metalc ? metalc7 D SG CYS 9 D CYS 52 1_555 N FE HEM . D HEM 1420 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? 
metalc ? metalc8 D NE2 HIS 22 D HIS 65 1_555 N FE HEM . D HEM 1420 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? 
metalc ? metalc9 E SG CYS 9 E CYS 52 1_555 P FE HEM . E HEM 1520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? 
metalc ? metalc10 E NE2 HIS 22 E HIS 65 1_555 P FE HEM . E HEM 1520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? 
metalc ? metalc11 F SG CYS 9 F CYS 52 1_555 R FE HEM . F HEM 1620 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.811 ? 
metalc ? metalc12 F NE2 HIS 22 F HIS 65 1_555 R FE HEM . F HEM 1620 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? 
#
_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' 
#
_atom_sites.entry_id                     1M54 
_atom_sites.fract_transf_matrix[1][1]    0.011663 
_atom_sites.fract_transf_matrix[1][2]    0.004854 
_atom_sites.fract_transf_matrix[1][3]    0.004117 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01265 
_atom_sites.fract_transf_matrix[2][3]    0.004197 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.011076 
_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
G 2 PLP A 1 1110 1110 PLP PLP . 
H 3 HEM A 1 1120 1120 HEM HEM . 
I 2 PLP B 1 1210 1210 PLP PLP . 
J 3 HEM B 1 1220 1220 HEM HEM . 
K 2 PLP C 1 1310 1310 PLP PLP . 
L 3 HEM C 1 1320 1320 HEM HEM . 
M 2 PLP D 1 1410 1410 PLP PLP . 
N 3 HEM D 1 1420 1420 HEM HEM . 
O 2 PLP E 1 1510 1510 PLP PLP . 
P 3 HEM E 1 1520 1520 HEM HEM . 
Q 2 PLP F 1 1610 1610 PLP PLP . 
R 3 HEM F 1 1620 1620 HEM HEM . 
S 4 HOH A 1 1121 4 HOH HOH . 
S 4 HOH A 2 1122 10 HOH HOH . 
S 4 HOH A 3 1123 25 HOH HOH . 
S 4 HOH A 4 1124 28 HOH HOH . 
S 4 HOH A 5 1125 31 HOH HOH . 
S 4 HOH A 6 1126 38 HOH HOH . 
S 4 HOH A 7 1127 42 HOH HOH . 
S 4 HOH A 8 1128 52 HOH HOH . 
S 4 HOH A 9 1129 53 HOH HOH . 
S 4 HOH A 10 1130 62 HOH HOH . 
S 4 HOH A 11 1131 76 HOH HOH . 
S 4 HOH A 12 1132 87 HOH HOH . 
T 4 HOH B 1 1221 1 HOH HOH . 
T 4 HOH B 2 1222 6 HOH HOH . 
T 4 HOH B 3 1223 7 HOH HOH . 
T 4 HOH B 4 1224 11 HOH HOH . 
T 4 HOH B 5 1225 13 HOH HOH . 
T 4 HOH B 6 1226 30 HOH HOH . 
T 4 HOH B 7 1227 34 HOH HOH . 
T 4 HOH B 8 1228 60 HOH HOH . 
T 4 HOH B 9 1229 66 HOH HOH . 
T 4 HOH B 10 1230 70 HOH HOH . 
T 4 HOH B 11 1231 78 HOH HOH . 
T 4 HOH B 12 1232 89 HOH HOH . 
U 4 HOH C 1 1321 17 HOH HOH . 
U 4 HOH C 2 1322 22 HOH HOH . 
U 4 HOH C 3 1323 27 HOH HOH . 
U 4 HOH C 4 1324 29 HOH HOH . 
U 4 HOH C 5 1325 35 HOH HOH . 
U 4 HOH C 6 1326 37 HOH HOH . 
U 4 HOH C 7 1327 46 HOH HOH . 
U 4 HOH C 8 1328 51 HOH HOH . 
U 4 HOH C 9 1329 63 HOH HOH . 
U 4 HOH C 10 1330 72 HOH HOH . 
U 4 HOH C 11 1331 81 HOH HOH . 
U 4 HOH C 12 1332 91 HOH HOH . 
U 4 HOH C 13 1333 99 HOH HOH . 
U 4 HOH C 14 1334 100 HOH HOH . 
V 4 HOH D 1 1421 2 HOH HOH . 
V 4 HOH D 2 1422 5 HOH HOH . 
V 4 HOH D 3 1423 16 HOH HOH . 
V 4 HOH D 4 1424 21 HOH HOH . 
V 4 HOH D 5 1425 32 HOH HOH . 
V 4 HOH D 6 1426 36 HOH HOH . 
V 4 HOH D 7 1427 43 HOH HOH . 
V 4 HOH D 8 1428 44 HOH HOH . 
V 4 HOH D 9 1429 45 HOH HOH . 
V 4 HOH D 10 1430 50 HOH HOH . 
V 4 HOH D 11 1431 54 HOH HOH . 
V 4 HOH D 12 1432 58 HOH HOH . 
V 4 HOH D 13 1433 59 HOH HOH . 
V 4 HOH D 14 1434 67 HOH HOH . 
V 4 HOH D 15 1435 71 HOH HOH . 
V 4 HOH D 16 1436 74 HOH HOH . 
V 4 HOH D 17 1437 79 HOH HOH . 
V 4 HOH D 18 1438 80 HOH HOH . 
V 4 HOH D 19 1439 82 HOH HOH . 
V 4 HOH D 20 1440 83 HOH HOH . 
V 4 HOH D 21 1441 85 HOH HOH . 
V 4 HOH D 22 1442 90 HOH HOH . 
V 4 HOH D 23 1443 94 HOH HOH . 
V 4 HOH D 24 1444 97 HOH HOH . 
V 4 HOH D 25 1445 98 HOH HOH . 
V 4 HOH D 26 1446 102 HOH HOH . 
W 4 HOH E 1 1521 3 HOH HOH . 
W 4 HOH E 2 1522 8 HOH HOH . 
W 4 HOH E 3 1523 9 HOH HOH . 
W 4 HOH E 4 1524 15 HOH HOH . 
W 4 HOH E 5 1525 19 HOH HOH . 
W 4 HOH E 6 1526 20 HOH HOH . 
W 4 HOH E 7 1527 23 HOH HOH . 
W 4 HOH E 8 1528 26 HOH HOH . 
W 4 HOH E 9 1529 39 HOH HOH . 
W 4 HOH E 10 1530 40 HOH HOH . 
W 4 HOH E 11 1531 48 HOH HOH . 
W 4 HOH E 12 1532 49 HOH HOH . 
W 4 HOH E 13 1533 55 HOH HOH . 
W 4 HOH E 14 1534 61 HOH HOH . 
W 4 HOH E 15 1535 65 HOH HOH . 
W 4 HOH E 16 1536 68 HOH HOH . 
W 4 HOH E 17 1537 75 HOH HOH . 
W 4 HOH E 18 1538 84 HOH HOH . 
W 4 HOH E 19 1539 88 HOH HOH . 
W 4 HOH E 20 1540 93 HOH HOH . 
W 4 HOH E 21 1541 95 HOH HOH . 
W 4 HOH E 22 1542 96 HOH HOH . 
W 4 HOH E 23 1543 101 HOH HOH . 
W 4 HOH E 24 1544 103 HOH HOH . 
X 4 HOH F 1 1621 12 HOH HOH . 
X 4 HOH F 2 1622 14 HOH HOH . 
X 4 HOH F 3 1623 18 HOH HOH . 
X 4 HOH F 4 1624 24 HOH HOH . 
X 4 HOH F 5 1625 33 HOH HOH . 
X 4 HOH F 6 1626 41 HOH HOH . 
X 4 HOH F 7 1627 47 HOH HOH . 
X 4 HOH F 8 1628 56 HOH HOH . 
X 4 HOH F 9 1629 57 HOH HOH . 
X 4 HOH F 10 1630 64 HOH HOH . 
X 4 HOH F 11 1631 69 HOH HOH . 
X 4 HOH F 12 1632 73 HOH HOH . 
X 4 HOH F 13 1633 77 HOH HOH . 
X 4 HOH F 14 1634 86 HOH HOH . 
X 4 HOH F 15 1635 92 HOH HOH . 
X 4 HOH F 16 1636 104 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 . . . G 2 5.355 -5.286 13.892 1 21.2 ? N1 PLP 1110 A 1 
HETATM 2 C C2 PLP . . . G 2 5.731 -4.166 13.166 1 22.41 ? C2 PLP 1110 A 1 
HETATM 3 C C2A PLP . . . G 2 6.257 -4.334 11.745 1 23.73 ? C2A PLP 1110 A 1 
HETATM 4 C C3 PLP . . . G 2 5.618 -2.9 13.75 1 21.88 ? C3 PLP 1110 A 1 
HETATM 5 O O3 PLP . . . G 2 5.989 -1.776 13.036 1 23.99 ? O3 PLP 1110 A 1 
HETATM 6 C C4 PLP . . . G 2 5.125 -2.777 15.064 1 18.69 ? C4 PLP 1110 A 1 
HETATM 7 C C4A PLP . . . G 2 5.015 -1.379 15.641 1 19.09 ? C4A PLP 1110 A 1 
HETATM 8 C C5 PLP . . . G 2 4.742 -3.948 15.799 1 17.12 ? C5 PLP 1110 A 1 
HETATM 9 C C6 PLP . . . G 2 4.869 -5.176 15.189 1 19.53 ? C6 PLP 1110 A 1 
HETATM 10 C C5A PLP . . . G 2 4.191 -3.942 17.238 1 15.7 ? C5A PLP 1110 A 1 
HETATM 11 O O4P PLP . . . G 2 3.195 -2.959 17.454 1 17.09 ? O4P PLP 1110 A 1 
HETATM 12 P P PLP . . . G 2 3.229 -2.056 18.798 1 19.37 ? P PLP 1110 A 1 
HETATM 13 O O1P PLP . . . G 2 2.085 -1.109 18.751 1 14.75 ? O1P PLP 1110 A 1 
HETATM 14 O O2P PLP . . . G 2 3.031 -3.106 19.987 1 16.39 ? O2P PLP 1110 A 1 
HETATM 15 O O3P PLP . . . G 2 4.597 -1.52 18.909 1 19.99 ? O3P PLP 1110 A 1 
#
_model_server_stats.io_time_ms              78 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    26 
_model_server_stats.query_time_ms           425 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           15 
#