data_5HVM
#
_model_server_result.job_id            iaq-P5BVWT6XPOoOqXNH-Q 
_model_server_result.datetime_utc      '2024-11-08 19:58:20' 
_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          5hvm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":602}' 
#
_entry.id    5HVM 
#
_exptl.entry_id    5HVM 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              335.35 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (1S,2S,3R,6S)-4-(HYDROXYMETHYL)-6-{[(1S,2S,3S,4R,5R)-2,3,4-TRIHYDROXY-5-(HYDROXYMETHYL)CYCLOHEXYL]AMINO}CYCLOHEX-4-ENE-1,2,3-TRIOL 
_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            5HVM 
_cell.length_a            83.915 
_cell.length_b            101.153 
_cell.length_c            146.992 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5HVM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 2 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? dimeric 2 author_defined_assembly 1 
PISA tetrameric 4 software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F,G,H 1 1 
A,B,C,D,E,F,G,H 2 1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 F N N 
#
_chem_comp.formula           'C14 H25 N O8' 
_chem_comp.formula_weight    335.35 
_chem_comp.id                VDM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (1S,2S,3R,6S)-4-(HYDROXYMETHYL)-6-{[(1S,2S,3S,4R,5R)-2,3,4-TRIHYDROXY-5-(HYDROXYMETHYL)CYCLOHEXYL]AMINO}CYCLOHEX-4-ENE-1,2,3-TRIOL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     VALIDOXYLAMINE 
#
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
O7 C7 VDM sing 416 n n 
O7 H7 VDM sing 417 n n 
C7 C5 VDM sing 418 n n 
C7 H7C1 VDM sing 419 n n 
C7 H7C2 VDM sing 420 n n 
C5 C6 VDM doub 421 n n 
C5 C4 VDM sing 422 n n 
C6 C1 VDM sing 423 n n 
C6 H6 VDM sing 424 n n 
C4 O4 VDM sing 425 n n 
C4 C3 VDM sing 426 n n 
C4 H4 VDM sing 427 n n 
O4 HA VDM sing 428 n n 
C3 O3 VDM sing 429 n n 
C3 C2 VDM sing 430 n n 
C3 H3 VDM sing 431 n n 
O3 HB VDM sing 432 n n 
C2 O2 VDM sing 433 n n 
C2 C1 VDM sing 434 n n 
C2 H2 VDM sing 435 n n 
O2 HC VDM sing 436 n n 
C1 N1' VDM sing 437 n n 
C1 H1 VDM sing 438 n n 
N1' C1' VDM sing 439 n n 
N1' H1' VDM sing 440 n n 
C1' HD VDM sing 441 n n 
C1' C2' VDM sing 442 n n 
C1' C6' VDM sing 443 n n 
C2' H2' VDM sing 444 n n 
C2' O2' VDM sing 445 n n 
C2' C3' VDM sing 446 n n 
O2' HE VDM sing 447 n n 
C6' "H6'1" VDM sing 448 n n 
C6' "H6'2" VDM sing 449 n n 
C6' C5' VDM sing 450 n n 
C5' H5' VDM sing 451 n n 
C5' C7' VDM sing 452 n n 
C5' C4' VDM sing 453 n n 
C7' "H7'1" VDM sing 454 n n 
C7' "H7'2" VDM sing 455 n n 
C7' O7' VDM sing 456 n n 
O7' H7' VDM sing 457 n n 
C4' H4' VDM sing 458 n n 
C4' O4' VDM sing 459 n n 
C4' C3' VDM sing 460 n n 
O4' HF VDM sing 461 n n 
C3' H3' VDM sing 462 n n 
C3' O3' VDM sing 463 n n 
O3' HG VDM sing 464 n n 
#
_atom_sites.entry_id                     5HVM 
_atom_sites.fract_transf_matrix[1][1]    0.011917 
_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]    0.009886 
_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]    0.006803 
_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
C 2 UDP A 1 601 601 UDP UDP . 
D 3 VDM A 1 602 602 VDM VDM . 
E 2 UDP B 1 601 601 UDP UDP . 
F 3 VDM B 1 602 602 VDM VDM . 
G 4 HOH A 1 701 5 HOH HOH . 
G 4 HOH A 2 702 3 HOH HOH . 
G 4 HOH A 3 703 2 HOH HOH . 
G 4 HOH A 4 704 6 HOH HOH . 
G 4 HOH A 5 705 1 HOH HOH . 
G 4 HOH A 6 706 7 HOH HOH . 
H 4 HOH B 1 701 8 HOH HOH . 
H 4 HOH B 2 702 4 HOH HOH . 
H 4 HOH B 3 703 9 HOH HOH . 
H 4 HOH B 4 704 10 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 O O7 VDM . . . F 3 2.039 15.167 20.483 1 80.1 ? O7 VDM 602 B 1 
HETATM 2 C C7 VDM . . . F 3 3.259 15.901 20.43 1 66.64 ? C7 VDM 602 B 1 
HETATM 3 C C5 VDM . . . F 3 2.931 17.322 20.112 1 53.51 ? C5 VDM 602 B 1 
HETATM 4 C C6 VDM . . . F 3 3.635 17.98 19.183 1 64.29 ? C6 VDM 602 B 1 
HETATM 5 C C4 VDM . . . F 3 1.785 17.935 20.849 1 60.83 ? C4 VDM 602 B 1 
HETATM 6 O O4 VDM . . . F 3 1.873 17.536 22.211 1 59.01 ? O4 VDM 602 B 1 
HETATM 7 C C3 VDM . . . F 3 1.783 19.445 20.776 1 62.31 ? C3 VDM 602 B 1 
HETATM 8 O O3 VDM . . . F 3 0.516 19.917 21.198 1 56.69 ? O3 VDM 602 B 1 
HETATM 9 C C2 VDM . . . F 3 2.012 19.911 19.36 1 62.15 ? C2 VDM 602 B 1 
HETATM 10 O O2 VDM . . . F 3 1.923 21.325 19.388 1 74.98 ? O2 VDM 602 B 1 
HETATM 11 C C1 VDM . . . F 3 3.343 19.415 18.777 1 76.11 ? C1 VDM 602 B 1 
HETATM 12 N N1' VDM . . . F 3 4.486 20.261 19.102 1 80 ? N1' VDM 602 B 1 
HETATM 13 C C1' VDM . . . F 3 4.725 21.55 18.474 1 63.78 ? C1' VDM 602 B 1 
HETATM 14 C C2' VDM . . . F 3 5.489 21.46 17.181 1 61.65 ? C2' VDM 602 B 1 
HETATM 15 O O2' VDM . . . F 3 5.257 20.163 16.664 1 66.92 ? O2' VDM 602 B 1 
HETATM 16 C C6' VDM . . . F 3 5.342 22.502 19.469 1 53.74 ? C6' VDM 602 B 1 
HETATM 17 C C5' VDM . . . F 3 6.933 22.744 19.565 1 53.75 ? C5' VDM 602 B 1 
HETATM 18 C C7' VDM . . . F 3 7.258 24.019 20.279 1 58.29 ? C7' VDM 602 B 1 
HETATM 19 O O7' VDM . . . F 3 6.715 23.961 21.585 1 69.68 ? O7' VDM 602 B 1 
HETATM 20 C C4' VDM . . . F 3 7.382 22.802 18.026 1 52.76 ? C4' VDM 602 B 1 
HETATM 21 O O4' VDM . . . F 3 8.795 22.798 17.969 1 58.81 ? O4' VDM 602 B 1 
HETATM 22 C C3' VDM . . . F 3 6.926 21.63 17.21 1 61.63 ? C3' VDM 602 B 1 
HETATM 23 O O3' VDM . . . F 3 7.414 21.781 15.882 1 66.39 ? O3' VDM 602 B 1 
HETATM 24 H H7 VDM . . . F 3 1.474 15.54 21.173 1 96.12 ? H7 VDM 602 B 1 
HETATM 25 H H7C1 VDM . . . F 3 3.911 15.486 19.661 1 79.97 ? H7C1 VDM 602 B 1 
HETATM 26 H H7C2 VDM . . . F 3 3.768 15.845 21.392 1 79.97 ? H7C2 VDM 602 B 1 
HETATM 27 H H6 VDM . . . F 3 4.444 17.466 18.696 1 77.15 ? H6 VDM 602 B 1 
HETATM 28 H H4 VDM . . . F 3 0.844 17.567 20.422 1 72.99 ? H4 VDM 602 B 1 
HETATM 29 H H1 VDM . . . F 3 3.236 19.43 17.685 1 91.33 ? H1 VDM 602 B 1 
HETATM 30 H HA VDM . . . F 3 1.799 16.575 22.266 1 70.82 ? HA VDM 602 B 1 
HETATM 31 H H3 VDM . . . F 3 2.577 19.841 21.421 1 74.77 ? H3 VDM 602 B 1 
HETATM 32 H HB VDM . . . F 3 0.241 19.435 21.988 1 68.03 ? HB VDM 602 B 1 
HETATM 33 H H2 VDM . . . F 3 1.199 19.511 18.744 1 74.58 ? H2 VDM 602 B 1 
HETATM 34 H HC VDM . . . F 3 1.062 21.588 19.739 1 89.98 ? HC VDM 602 B 1 
HETATM 35 H H1' VDM . . . F 3 5.144 19.937 19.794 1 96 ? H1' VDM 602 B 1 
HETATM 36 H HD VDM . . . F 3 3.757 21.974 18.195 1 76.54 ? HD VDM 602 B 1 
HETATM 37 H H2' VDM . . . F 3 5.078 22.203 16.488 1 73.98 ? H2' VDM 602 B 1 
HETATM 38 H "H6'1" VDM . . . F 3 4.883 23.477 19.303 1 64.49 ? "H6'1" VDM 602 B 1 
HETATM 39 H "H6'2" VDM . . . F 3 5.013 22.18 20.457 1 64.49 ? "H6'2" VDM 602 B 1 
HETATM 40 H HE VDM . . . F 3 5.672 20.095 15.795 1 80.31 ? HE VDM 602 B 1 
HETATM 41 H H3' VDM . . . F 3 7.358 20.724 17.65 1 73.95 ? H3' VDM 602 B 1 
HETATM 42 H H5' VDM . . . F 3 7.415 21.896 20.065 1 64.5 ? H5' VDM 602 B 1 
HETATM 43 H "H7'1" VDM . . . F 3 6.833 24.864 19.739 1 69.95 ? "H7'1" VDM 602 B 1 
HETATM 44 H "H7'2" VDM . . . F 3 8.338 24.15 20.329 1 69.95 ? "H7'2" VDM 602 B 1 
HETATM 45 H H4' VDM . . . F 3 6.988 23.719 17.575 1 63.31 ? H4' VDM 602 B 1 
HETATM 46 H H7' VDM . . . F 3 5.865 24.42 21.592 1 83.62 ? H7' VDM 602 B 1 
HETATM 47 H HF VDM . . . F 3 9.138 22.217 18.659 1 70.57 ? HF VDM 602 B 1 
HETATM 48 H HG VDM . . . F 3 6.859 22.412 15.407 1 79.67 ? HG VDM 602 B 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           334 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           48 
#