data_2VMY # _model_server_result.job_id o47Z-BatJBlsnvnIan5XCA _model_server_result.datetime_utc '2024-11-24 17:07:06' _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 2vmy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":701}' # _entry.id 2VMY # _exptl.entry_id 2VMY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 118.174 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (4R)-2-METHYLPENTANE-2,4-DIOL _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90.33 _cell.angle_gamma 90 _cell.entry_id 2VMY _cell.length_a 57.382 _cell.length_b 103.483 _cell.length_c 61.959 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VMY _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id I _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 D C4A PLP . A PLP 501 1_555 C N GLY . A GLY 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.233 ? covale ? covale2 G C4A PLP . B PLP 501 1_555 F N GLY . B GLY 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.23 ? # _chem_comp.formula 'C6 H14 O2' _chem_comp.formula_weight 118.174 _chem_comp.id MRD _chem_comp.mon_nstd_flag . _chem_comp.name (4R)-2-METHYLPENTANE-2,4-DIOL _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 C1 C2 MRD sing 296 n n C1 H1C1 MRD sing 297 n n C1 H1C2 MRD sing 298 n n C1 H1C3 MRD sing 299 n n C2 O2 MRD sing 300 n n C2 CM MRD sing 301 n n C2 C3 MRD sing 302 n n O2 H2 MRD sing 303 n n CM HMC1 MRD sing 304 n n CM HMC2 MRD sing 305 n n CM HMC3 MRD sing 306 n n C3 C4 MRD sing 307 n n C3 H3C1 MRD sing 308 n n C3 H3C2 MRD sing 309 n n C4 O4 MRD sing 310 n n C4 C5 MRD sing 311 n n C4 H4 MRD sing 312 n n O4 HA MRD sing 313 n n C5 H5C1 MRD sing 314 n n C5 H5C2 MRD sing 315 n n C5 H5C3 MRD sing 316 n n # _atom_sites.entry_id 2VMY _atom_sites.fract_transf_matrix[1][1] 0.017427 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.0001 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009663 _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] 0.01614 _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 GLY A 1 502 502 GLY GLY . D 3 PLP A 1 501 501 PLP PLP . E 4 FFO A 1 505 505 FFO FFO . F 2 GLY B 1 502 502 GLY GLY . G 3 PLP B 1 501 501 PLP PLP . H 4 FFO B 1 505 505 FFO FFO . I 5 MRD B 1 701 701 MRD MRD . J 6 HOH A 1 2001 2001 HOH HOH . J 6 HOH A 2 2002 2002 HOH HOH . J 6 HOH A 3 2003 2003 HOH HOH . J 6 HOH A 4 2004 2004 HOH HOH . J 6 HOH A 5 2005 2005 HOH HOH . J 6 HOH A 6 2006 2006 HOH HOH . J 6 HOH A 7 2007 2007 HOH HOH . J 6 HOH A 8 2008 2008 HOH HOH . J 6 HOH A 9 2009 2009 HOH HOH . J 6 HOH A 10 2010 2010 HOH HOH . J 6 HOH A 11 2011 2011 HOH HOH . J 6 HOH A 12 2012 2012 HOH HOH . K 6 HOH B 1 2001 2001 HOH HOH . K 6 HOH B 2 2002 2002 HOH HOH . K 6 HOH B 3 2003 2003 HOH HOH . K 6 HOH B 4 2004 2004 HOH HOH . K 6 HOH B 5 2005 2005 HOH HOH . K 6 HOH B 6 2006 2006 HOH HOH . K 6 HOH B 7 2007 2007 HOH HOH . K 6 HOH B 8 2008 2008 HOH HOH . K 6 HOH B 9 2009 2009 HOH HOH . K 6 HOH B 10 2010 2010 HOH HOH . K 6 HOH B 11 2011 2011 HOH HOH . K 6 HOH B 12 2012 2012 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 C C1 MRD . . . I 5 31.03 11.514 16.393 1 57.51 ? C1 MRD 701 B 1 HETATM 2 C C2 MRD . . . I 5 32.181 10.561 16.692 1 57.71 ? C2 MRD 701 B 1 HETATM 3 O O2 MRD . . . I 5 33.425 11.191 16.293 1 57.92 ? O2 MRD 701 B 1 HETATM 4 C CM MRD . . . I 5 32.246 10.352 18.198 1 57.89 ? CM MRD 701 B 1 HETATM 5 C C3 MRD . . . I 5 32.002 9.199 16.004 1 57.44 ? C3 MRD 701 B 1 HETATM 6 C C4 MRD . . . I 5 32.252 9.096 14.491 1 57.45 ? C4 MRD 701 B 1 HETATM 7 O O4 MRD . . . I 5 32.865 10.247 13.948 1 57.3 ? O4 MRD 701 B 1 HETATM 8 C C5 MRD . . . I 5 30.953 8.832 13.74 1 57.09 ? C5 MRD 701 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 8 #