data_6YRQ # _model_server_result.job_id tESq6t_T4b1OzPVkTrJyTA _model_server_result.datetime_utc '2025-07-12 21:18:29' _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 6yrq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":603}' # _entry.id 6YRQ # _exptl.entry_id 6YRQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 118.174 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (4S)-2-METHYL-2,4-PENTANEDIOL _entity.pdbx_number_of_molecules 4 _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 6YRQ _cell.length_a 90.636 _cell.length_b 123.056 _cell.length_c 90.119 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YRQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _pdbx_struct_assembly.details author_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,L,M,N,O,P,Q,R,S,T,U,V,W _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 L N N ? 6 M N N ? 6 N N N ? 6 O N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n I NAG 1 I 1 NAG C 1481 NAG 3 n I NAG 2 I 2 NAG C 1482 NAG 4 n J NAG 1 J 1 NAG D 484 NAG 4 n J NAG 2 J 2 NAG D 485 NAG 4 n J BMA 3 J 3 BMA D 486 BMA # 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 disulf ? disulf1 A SG CYS 5 A CYS 379 1_555 A SG CYS 64 A CYS 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 9 A CYS 383 1_555 A SG CYS 18 A CYS 392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf3 A SG CYS 34 A CYS 408 1_555 A SG CYS 53 A CYS 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf4 A SG CYS 81 A CYS 455 1_555 A SG CYS 104 A CYS 478 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf5 B SG CYS 5 B CYS 379 1_555 B SG CYS 64 B CYS 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf6 B SG CYS 9 B CYS 383 1_555 B SG CYS 18 B CYS 392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf7 B SG CYS 34 B CYS 408 1_555 B SG CYS 53 B CYS 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf8 B SG CYS 81 B CYS 455 1_555 B SG CYS 104 B CYS 478 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf9 C SG CYS 5 C CYS 379 1_555 C SG CYS 64 C CYS 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf10 C SG CYS 9 C CYS 383 1_555 C SG CYS 18 C CYS 392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf11 C SG CYS 34 C CYS 408 1_555 C SG CYS 53 C CYS 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf12 C SG CYS 81 C CYS 455 1_555 C SG CYS 104 C CYS 478 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf13 D SG CYS 5 D CYS 379 1_555 D SG CYS 64 D CYS 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf14 D SG CYS 9 D CYS 383 1_555 D SG CYS 18 D CYS 392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf15 D SG CYS 34 D CYS 408 1_555 D SG CYS 53 D CYS 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf16 D SG CYS 81 D CYS 455 1_555 D SG CYS 104 D CYS 478 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 A ND2 ASN 28 A ASN 402 1_555 K C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale2 C ND2 ASN 28 C ASN 402 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 D ND2 ASN 28 D ASN 402 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale4 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale5 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale6 J O4 NAG . J NAG 2 1_555 J C1 BMA . J BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? # _chem_comp.formula 'C6 H14 O2' _chem_comp.formula_weight 118.174 _chem_comp.id MPD _chem_comp.mon_nstd_flag . _chem_comp.name (4S)-2-METHYL-2,4-PENTANEDIOL _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 MPD sing 300 n n C1 H11 MPD sing 301 n n C1 H12 MPD sing 302 n n C1 H13 MPD sing 303 n n C2 O2 MPD sing 304 n n C2 CM MPD sing 305 n n C2 C3 MPD sing 306 n n O2 HO2 MPD sing 307 n n CM HM1 MPD sing 308 n n CM HM2 MPD sing 309 n n CM HM3 MPD sing 310 n n C3 C4 MPD sing 311 n n C3 H31 MPD sing 312 n n C3 H32 MPD sing 313 n n C4 O4 MPD sing 314 n n C4 C5 MPD sing 315 n n C4 H4 MPD sing 316 n n O4 HO4 MPD sing 317 n n C5 H51 MPD sing 318 n n C5 H52 MPD sing 319 n n C5 H53 MPD sing 320 n n # _atom_sites.entry_id 6YRQ _atom_sites.fract_transf_matrix[1][1] 0.011033 _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] 0.008126 _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] 0.011096 _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 K 5 NAG A 1 601 1481 NAG NAG . L 6 MPD A 1 602 1 MPD MPD . M 6 MPD B 1 601 3 MPD MPD . N 6 MPD C 1 603 2 MPD MPD . O 6 MPD D 1 604 4 MPD MPD . P 7 HOH A 1 701 28 HOH HOH . P 7 HOH A 2 702 94 HOH HOH . P 7 HOH A 3 703 75 HOH HOH . P 7 HOH A 4 704 27 HOH HOH . P 7 HOH A 5 705 52 HOH HOH . P 7 HOH A 6 706 77 HOH HOH . P 7 HOH A 7 707 60 HOH HOH . P 7 HOH A 8 708 17 HOH HOH . P 7 HOH A 9 709 123 HOH HOH . P 7 HOH A 10 710 135 HOH HOH . P 7 HOH A 11 711 131 HOH HOH . P 7 HOH A 12 712 89 HOH HOH . P 7 HOH A 13 713 61 HOH HOH . P 7 HOH A 14 714 53 HOH HOH . P 7 HOH A 15 715 108 HOH HOH . P 7 HOH A 16 716 35 HOH HOH . P 7 HOH A 17 717 36 HOH HOH . P 7 HOH A 18 718 10 HOH HOH . P 7 HOH A 19 719 8 HOH HOH . P 7 HOH A 20 720 45 HOH HOH . P 7 HOH A 21 721 111 HOH HOH . P 7 HOH A 22 722 130 HOH HOH . P 7 HOH A 23 723 120 HOH HOH . P 7 HOH A 24 724 106 HOH HOH . P 7 HOH A 25 725 114 HOH HOH . Q 7 HOH B 1 701 87 HOH HOH . Q 7 HOH B 2 702 73 HOH HOH . Q 7 HOH B 3 703 7 HOH HOH . Q 7 HOH B 4 704 110 HOH HOH . Q 7 HOH B 5 705 58 HOH HOH . Q 7 HOH B 6 706 72 HOH HOH . Q 7 HOH B 7 707 37 HOH HOH . Q 7 HOH B 8 708 59 HOH HOH . Q 7 HOH B 9 709 86 HOH HOH . Q 7 HOH B 10 710 3 HOH HOH . Q 7 HOH B 11 711 121 HOH HOH . Q 7 HOH B 12 712 29 HOH HOH . Q 7 HOH B 13 713 95 HOH HOH . Q 7 HOH B 14 714 23 HOH HOH . Q 7 HOH B 15 715 42 HOH HOH . Q 7 HOH B 16 716 25 HOH HOH . Q 7 HOH B 17 717 56 HOH HOH . Q 7 HOH B 18 718 24 HOH HOH . Q 7 HOH B 19 719 68 HOH HOH . Q 7 HOH B 20 720 91 HOH HOH . Q 7 HOH B 21 721 14 HOH HOH . Q 7 HOH B 22 722 102 HOH HOH . Q 7 HOH B 23 723 124 HOH HOH . Q 7 HOH B 24 724 129 HOH HOH . Q 7 HOH B 25 725 31 HOH HOH . Q 7 HOH B 26 726 97 HOH HOH . Q 7 HOH B 27 727 101 HOH HOH . Q 7 HOH B 28 728 67 HOH HOH . Q 7 HOH B 29 729 84 HOH HOH . Q 7 HOH B 30 730 105 HOH HOH . Q 7 HOH B 31 731 117 HOH HOH . Q 7 HOH B 32 732 99 HOH HOH . R 7 HOH C 1 701 76 HOH HOH . R 7 HOH C 2 702 132 HOH HOH . R 7 HOH C 3 703 93 HOH HOH . R 7 HOH C 4 704 78 HOH HOH . R 7 HOH C 5 705 88 HOH HOH . R 7 HOH C 6 706 69 HOH HOH . R 7 HOH C 7 707 33 HOH HOH . R 7 HOH C 8 708 21 HOH HOH . R 7 HOH C 9 709 83 HOH HOH . R 7 HOH C 10 710 46 HOH HOH . R 7 HOH C 11 711 66 HOH HOH . R 7 HOH C 12 712 122 HOH HOH . R 7 HOH C 13 713 79 HOH HOH . R 7 HOH C 14 714 15 HOH HOH . R 7 HOH C 15 715 54 HOH HOH . R 7 HOH C 16 716 47 HOH HOH . R 7 HOH C 17 717 34 HOH HOH . R 7 HOH C 18 718 57 HOH HOH . R 7 HOH C 19 719 5 HOH HOH . R 7 HOH C 20 720 38 HOH HOH . R 7 HOH C 21 721 51 HOH HOH . R 7 HOH C 22 722 11 HOH HOH . R 7 HOH C 23 723 18 HOH HOH . R 7 HOH C 24 724 80 HOH HOH . R 7 HOH C 25 725 85 HOH HOH . R 7 HOH C 26 726 71 HOH HOH . R 7 HOH C 27 727 50 HOH HOH . R 7 HOH C 28 728 100 HOH HOH . R 7 HOH C 29 729 81 HOH HOH . S 7 HOH D 1 701 43 HOH HOH . S 7 HOH D 2 702 12 HOH HOH . S 7 HOH D 3 703 136 HOH HOH . S 7 HOH D 4 704 41 HOH HOH . S 7 HOH D 5 705 74 HOH HOH . S 7 HOH D 6 706 20 HOH HOH . S 7 HOH D 7 707 2 HOH HOH . S 7 HOH D 8 708 137 HOH HOH . S 7 HOH D 9 709 13 HOH HOH . S 7 HOH D 10 710 118 HOH HOH . S 7 HOH D 11 711 16 HOH HOH . S 7 HOH D 12 712 4 HOH HOH . S 7 HOH D 13 713 40 HOH HOH . S 7 HOH D 14 714 22 HOH HOH . S 7 HOH D 15 715 39 HOH HOH . S 7 HOH D 16 716 109 HOH HOH . S 7 HOH D 17 717 55 HOH HOH . S 7 HOH D 18 718 96 HOH HOH . S 7 HOH D 19 719 48 HOH HOH . S 7 HOH D 20 720 70 HOH HOH . S 7 HOH D 21 721 44 HOH HOH . S 7 HOH D 22 722 112 HOH HOH . S 7 HOH D 23 723 9 HOH HOH . S 7 HOH D 24 724 32 HOH HOH . S 7 HOH D 25 725 62 HOH HOH . S 7 HOH D 26 726 104 HOH HOH . S 7 HOH D 27 727 63 HOH HOH . S 7 HOH D 28 728 103 HOH HOH . S 7 HOH D 29 729 64 HOH HOH . S 7 HOH D 30 730 65 HOH HOH . S 7 HOH D 31 731 98 HOH HOH . S 7 HOH D 32 732 115 HOH HOH . S 7 HOH D 33 733 82 HOH HOH . S 7 HOH D 34 734 113 HOH HOH . S 7 HOH D 35 735 92 HOH HOH . S 7 HOH D 36 736 119 HOH HOH . T 7 HOH E 1 101 127 HOH HOH . T 7 HOH E 2 102 19 HOH HOH . U 7 HOH F 1 101 90 HOH HOH . U 7 HOH F 2 102 30 HOH HOH . U 7 HOH F 3 103 6 HOH HOH . U 7 HOH F 4 104 49 HOH HOH . U 7 HOH F 5 105 133 HOH HOH . V 7 HOH G 1 101 107 HOH HOH . V 7 HOH G 2 102 128 HOH HOH . V 7 HOH G 3 103 1 HOH HOH . V 7 HOH G 4 104 134 HOH HOH . W 7 HOH H 1 101 116 HOH HOH . W 7 HOH H 2 102 26 HOH HOH . W 7 HOH H 3 103 125 HOH HOH . W 7 HOH H 4 104 126 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 MPD . . . N 6 29.138 23.242 2.854 1 56.62 ? C1 MPD 603 C 1 HETATM 2 C C2 MPD . . . N 6 28.162 24.025 3.709 1 69.68 ? C2 MPD 603 C 1 HETATM 3 O O2 MPD . . . N 6 28.893 24.381 4.909 1 74.56 ? O2 MPD 603 C 1 HETATM 4 C CM MPD . . . N 6 26.995 23.141 4.131 1 70.25 ? CM MPD 603 C 1 HETATM 5 C C3 MPD . . . N 6 27.726 25.335 3.033 1 74.96 ? C3 MPD 603 C 1 HETATM 6 C C4 MPD . . . N 6 26.836 25.296 1.778 1 80.13 ? C4 MPD 603 C 1 HETATM 7 O O4 MPD . . . N 6 26.939 24.1 1.03 1 83.46 ? O4 MPD 603 C 1 HETATM 8 C C5 MPD . . . N 6 25.371 25.54 2.119 1 77.43 ? C5 MPD 603 C 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 8 #