data_5B1I
#
_model_server_result.job_id            GoWtm1ZRu_10OVJuPdCltQ 
_model_server_result.datetime_utc      '2024-11-02 03:29:06' 
_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          5b1i 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"U","auth_seq_id":401}' 
#
_entry.id    5B1I 
#
_exptl.entry_id    5B1I 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              378.338 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            N-[(3-HYDROXY-2-METHYL-5-{[(TRIHYDROXYPHOSPHORANYL)OXY]METHYL}PYRIDIN-4-YL)METHYLENE]METHIONINE 
_entity.pdbx_number_of_molecules    8 
_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            5B1I 
_cell.length_a            165.94 
_cell.length_b            165.94 
_cell.length_c            259.49 
_cell.Z_PDB               64 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5B1I 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
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 
PISA dimeric 2 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,I,J,K,L,M,N 1 1 
C,D,O,P,Q,R,S,T 2 1 
E,F,U,V,W,X,Y,Z 3 1 
G,H,AA,BA,CA,DA,EA,FA 4 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 I N N 
? 2 L N N 
? 2 O N N 
? 2 R N N 
? 2 U N N 
? 2 X N N 
? 2 AA N N 
? 2 DA N N 
#
_chem_comp.formula           'C13 H19 N2 O7 P S' 
_chem_comp.formula_weight    378.338 
_chem_comp.id                AA5 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              N-[(3-HYDROXY-2-METHYL-5-{[(TRIHYDROXYPHOSPHORANYL)OXY]METHYL}PYRIDIN-4-YL)METHYLENE]METHIONINE 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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
N CA AA5 sing 1 n n 
N C4A AA5 doub 2 n n 
CA C AA5 sing 3 n n 
CA CB AA5 sing 4 n n 
CA HA AA5 sing 5 n n 
C O1 AA5 doub 6 n n 
C O2 AA5 sing 7 n n 
CB CG AA5 sing 8 n n 
CB HB1 AA5 sing 9 n n 
CB HB2 AA5 sing 10 n n 
CG SD AA5 sing 11 n n 
CG HG1 AA5 sing 12 n n 
CG HG2 AA5 sing 13 n n 
SD CE AA5 sing 14 n n 
CE HE1 AA5 sing 15 n n 
CE HE2 AA5 sing 16 n n 
CE HE3 AA5 sing 17 n n 
O2 HO2 AA5 sing 18 n n 
C2 C2A AA5 sing 19 n n 
C2 C3 AA5 doub 20 n y 
C2 N1 AA5 sing 21 n y 
C2A H2A1 AA5 sing 22 n n 
C2A H2A2 AA5 sing 23 n n 
C2A H2A3 AA5 sing 24 n n 
C3 C4 AA5 sing 25 n y 
C3 O3 AA5 sing 26 n n 
C4 C4A AA5 sing 27 n n 
C4 C5 AA5 doub 28 n y 
C4A H4A AA5 sing 29 n n 
C5 C5A AA5 sing 30 n n 
C5 C6 AA5 sing 31 n y 
C5A O4P AA5 sing 32 n n 
C5A H5A1 AA5 sing 33 n n 
C5A H5A2 AA5 sing 34 n n 
C6 N1 AA5 doub 35 n y 
C6 H6 AA5 sing 36 n n 
O1P P AA5 doub 37 n n 
O2P P AA5 sing 38 n n 
O2P H2P AA5 sing 39 n n 
O3 HO3 AA5 sing 40 n n 
O3P P AA5 sing 41 n n 
O3P H3P AA5 sing 42 n n 
O4P P AA5 sing 43 n n 
#
_atom_sites.entry_id                     5B1I 
_atom_sites.fract_transf_matrix[1][1]    0.006026 
_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]    0.006026 
_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]    0.003854 
_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
I 2 AA5 A 1 401 401 AA5 AA5 . 
J 3 SO4 A 1 402 409 SO4 SO4 . 
K 3 SO4 A 1 403 417 SO4 SO4 . 
L 2 AA5 B 1 401 402 AA5 AA5 . 
M 3 SO4 B 1 402 410 SO4 SO4 . 
N 3 SO4 B 1 403 418 SO4 SO4 . 
O 2 AA5 C 1 401 403 AA5 AA5 . 
P 3 SO4 C 1 402 411 SO4 SO4 . 
Q 3 SO4 C 1 403 419 SO4 SO4 . 
R 2 AA5 D 1 401 404 AA5 AA5 . 
S 3 SO4 D 1 402 413 SO4 SO4 . 
T 3 SO4 D 1 403 421 SO4 SO4 . 
U 2 AA5 E 1 401 405 AA5 AA5 . 
V 3 SO4 E 1 402 412 SO4 SO4 . 
W 3 SO4 E 1 403 420 SO4 SO4 . 
X 2 AA5 F 1 401 406 AA5 AA5 . 
Y 3 SO4 F 1 402 414 SO4 SO4 . 
Z 3 SO4 F 1 403 422 SO4 SO4 . 
AA 2 AA5 G 1 401 407 AA5 AA5 . 
BA 3 SO4 G 1 402 415 SO4 SO4 . 
CA 3 SO4 G 1 403 423 SO4 SO4 . 
DA 2 AA5 H 1 401 408 AA5 AA5 . 
EA 3 SO4 H 1 402 416 SO4 SO4 . 
FA 3 SO4 H 1 403 424 SO4 SO4 . 
#
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 N AA5 . . . U 2 122.714 36.516 -31.441 1 54.98 ? N AA5 401 E 1 
HETATM 2 C CA AA5 . . . U 2 123.673 36.972 -30.419 1 53.1 ? CA AA5 401 E 1 
HETATM 3 C C AA5 . . . U 2 123.199 36.474 -29.067 1 53 ? C AA5 401 E 1 
HETATM 4 O O1 AA5 . . . U 2 122.352 35.526 -28.996 1 53.14 ? O1 AA5 401 E 1 
HETATM 5 C CB AA5 . . . U 2 123.782 38.537 -30.413 1 51.31 ? CB AA5 401 E 1 
HETATM 6 C CG AA5 . . . U 2 122.394 39.225 -30.385 1 48.13 ? CG AA5 401 E 1 
HETATM 7 S SD AA5 . . . U 2 122.545 40.969 -30.875 1 45.96 ? SD AA5 401 E 1 
HETATM 8 C CE AA5 . . . U 2 120.805 41.426 -31.122 1 45.22 ? CE AA5 401 E 1 
HETATM 9 O O2 AA5 . . . U 2 123.646 36.992 -28.005 1 52.31 ? O2 AA5 401 E 1 
HETATM 10 C C2 AA5 . . . U 2 119.776 35.226 -34.392 1 56.48 ? C2 AA5 401 E 1 
HETATM 11 C C2A AA5 . . . U 2 118.43 34.655 -34.034 1 56.05 ? C2A AA5 401 E 1 
HETATM 12 C C3 AA5 . . . U 2 120.686 35.564 -33.369 1 57.5 ? C3 AA5 401 E 1 
HETATM 13 C C4 AA5 . . . U 2 121.961 36.182 -33.745 1 57.83 ? C4 AA5 401 E 1 
HETATM 14 C C4A AA5 . . . U 2 122.951 36.643 -32.712 1 56.81 ? C4A AA5 401 E 1 
HETATM 15 C C5 AA5 . . . U 2 122.221 36.413 -35.158 1 57.57 ? C5 AA5 401 E 1 
HETATM 16 C C5A AA5 . . . U 2 123.498 37.131 -35.645 1 56.32 ? C5A AA5 401 E 1 
HETATM 17 C C6 AA5 . . . U 2 121.236 36.021 -36.082 1 57.7 ? C6 AA5 401 E 1 
HETATM 18 N N1 AA5 . . . U 2 120.075 35.455 -35.678 1 56.82 ? N1 AA5 401 E 1 
HETATM 19 O O1P AA5 . . . U 2 126.322 37.854 -36.727 1 53.23 ? O1P AA5 401 E 1 
HETATM 20 O O2P AA5 . . . U 2 127.138 36.159 -34.989 1 50.44 ? O2P AA5 401 E 1 
HETATM 21 O O3 AA5 . . . U 2 120.358 35.322 -32.058 1 57.79 ? O3 AA5 401 E 1 
HETATM 22 O O3P AA5 . . . U 2 125.764 38.19 -34.196 1 51.52 ? O3P AA5 401 E 1 
HETATM 23 O O4P AA5 . . . U 2 124.649 36.255 -35.557 1 54.68 ? O4P AA5 401 E 1 
HETATM 24 P P AA5 . . . U 2 125.967 37.117 -35.375 1 52.4 ? P AA5 401 E 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    32 
_model_server_stats.query_time_ms           280 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           24 
#