data_5HVM
#
_model_server_result.job_id            QYu1a5mTHGX2xmbMxEDeTA 
_model_server_result.datetime_utc      '2024-11-24 19:55:59' 
_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":"D","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 . . . D 3 19.591 -20.956 -7.787 1 92.43 ? O7 VDM 602 A 1 
HETATM 2 C C7 VDM . . . D 3 19.598 -21.551 -6.486 1 70.41 ? C7 VDM 602 A 1 
HETATM 3 C C5 VDM . . . D 3 19.091 -22.957 -6.58 1 52.52 ? C5 VDM 602 A 1 
HETATM 4 C C6 VDM . . . D 3 18.61 -23.544 -5.486 1 56.7 ? C6 VDM 602 A 1 
HETATM 5 C C4 VDM . . . D 3 19.136 -23.616 -7.917 1 65.57 ? C4 VDM 602 A 1 
HETATM 6 O O4 VDM . . . D 3 20.326 -23.196 -8.574 1 58.05 ? O4 VDM 602 A 1 
HETATM 7 C C3 VDM . . . D 3 19.131 -25.119 -7.806 1 70.7 ? C3 VDM 602 A 1 
HETATM 8 O O3 VDM . . . D 3 18.806 -25.687 -9.068 1 60.5 ? O3 VDM 602 A 1 
HETATM 9 C C2 VDM . . . D 3 18.072 -25.609 -6.853 1 54.49 ? C2 VDM 602 A 1 
HETATM 10 O O2 VDM . . . D 3 18.268 -27.015 -6.817 1 58.33 ? O2 VDM 602 A 1 
HETATM 11 C C1 VDM . . . D 3 18.055 -24.945 -5.464 1 60.31 ? C1 VDM 602 A 1 
HETATM 12 N N1' VDM . . . D 3 18.731 -25.674 -4.397 1 74.3 ? N1' VDM 602 A 1 
HETATM 13 C C1' VDM . . . D 3 18.425 -27.044 -4.032 1 58.02 ? C1' VDM 602 A 1 
HETATM 14 C C2' VDM . . . D 3 17.851 -27.165 -2.658 1 56.44 ? C2' VDM 602 A 1 
HETATM 15 O O2' VDM . . . D 3 17.305 -25.895 -2.345 1 56.84 ? O2' VDM 602 A 1 
HETATM 16 C C6' VDM . . . D 3 19.655 -27.869 -4.279 1 52.01 ? C6' VDM 602 A 1 
HETATM 17 C C5' VDM . . . D 3 20.539 -28.539 -3.12 1 51.2 ? C5' VDM 602 A 1 
HETATM 18 C C7' VDM . . . D 3 21.108 -29.847 -3.576 1 57.97 ? C7' VDM 602 A 1 
HETATM 19 O O7' VDM . . . D 3 21.931 -30.321 -2.53 1 69.55 ? O7' VDM 602 A 1 
HETATM 20 C C4' VDM . . . D 3 19.609 -28.677 -1.809 1 53.52 ? C4' VDM 602 A 1 
HETATM 21 O O4' VDM . . . D 3 20.452 -28.855 -0.69 1 52.33 ? O4' VDM 602 A 1 
HETATM 22 C C3' VDM . . . D 3 18.715 -27.498 -1.549 1 57.04 ? C3' VDM 602 A 1 
HETATM 23 O O3' VDM . . . D 3 17.926 -27.81 -0.412 1 54.9 ? O3' VDM 602 A 1 
HETATM 24 H H7 VDM . . . D 3 18.801 -21.23 -8.272 1 110.92 ? H7 VDM 602 A 1 
HETATM 25 H H7C1 VDM . . . D 3 18.965 -20.977 -5.809 1 84.49 ? H7C1 VDM 602 A 1 
HETATM 26 H H7C2 VDM . . . D 3 20.611 -21.554 -6.086 1 84.49 ? H7C2 VDM 602 A 1 
HETATM 27 H H6 VDM . . . D 3 18.617 -22.988 -4.566 1 68.04 ? H6 VDM 602 A 1 
HETATM 28 H H4 VDM . . . D 3 18.262 -23.305 -8.502 1 78.68 ? H4 VDM 602 A 1 
HETATM 29 H H1 VDM . . . D 3 17.001 -24.861 -5.174 1 72.38 ? H1 VDM 602 A 1 
HETATM 30 H HA VDM . . . D 3 20.098 -22.595 -9.295 1 69.66 ? HA VDM 602 A 1 
HETATM 31 H H3 VDM . . . D 3 20.116 -25.463 -7.467 1 84.84 ? H3 VDM 602 A 1 
HETATM 32 H HB VDM . . . D 3 19.262 -25.198 -9.765 1 72.6 ? HB VDM 602 A 1 
HETATM 33 H H2 VDM . . . D 3 17.103 -25.407 -7.323 1 65.38 ? H2 VDM 602 A 1 
HETATM 34 H HC VDM . . . D 3 19.18 -27.219 -6.577 1 69.99 ? HC VDM 602 A 1 
HETATM 35 H H1' VDM . . . D 3 19.452 -25.195 -3.877 1 89.16 ? H1' VDM 602 A 1 
HETATM 36 H HD VDM . . . D 3 17.623 -27.422 -4.67 1 69.62 ? HD VDM 602 A 1 
HETATM 37 H H2' VDM . . . D 3 17.044 -27.905 -2.689 1 67.73 ? H2' VDM 602 A 1 
HETATM 38 H "H6'1" VDM . . . D 3 20.34 -27.26 -4.871 1 62.41 ? "H6'1" VDM 602 A 1 
HETATM 39 H "H6'2" VDM . . . D 3 19.348 -28.682 -4.937 1 62.41 ? "H6'2" VDM 602 A 1 
HETATM 40 H HE VDM . . . D 3 16.567 -26.015 -1.734 1 68.21 ? HE VDM 602 A 1 
HETATM 41 H H3' VDM . . . D 3 19.347 -26.629 -1.33 1 68.45 ? H3' VDM 602 A 1 
HETATM 42 H H5' VDM . . . D 3 21.371 -27.866 -2.882 1 61.44 ? H5' VDM 602 A 1 
HETATM 43 H "H7'1" VDM . . . D 3 21.695 -29.708 -4.484 1 69.57 ? "H7'1" VDM 602 A 1 
HETATM 44 H "H7'2" VDM . . . D 3 20.306 -30.558 -3.777 1 69.57 ? "H7'2" VDM 602 A 1 
HETATM 45 H H4' VDM . . . D 3 18.975 -29.562 -1.932 1 64.22 ? H4' VDM 602 A 1 
HETATM 46 H H7' VDM . . . D 3 21.373 -30.624 -1.803 1 83.46 ? H7' VDM 602 A 1 
HETATM 47 H HF VDM . . . D 3 19.922 -28.803 0.116 1 62.8 ? HF VDM 602 A 1 
HETATM 48 H HG VDM . . . D 3 17.545 -28.691 -0.517 1 65.88 ? HG VDM 602 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           301 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           48 
#