data_6P6D # _model_server_result.job_id v-uE-vxDPyVcMowudBQZcw _model_server_result.datetime_utc '2024-10-19 23:52:33' _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 6p6d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":609}' # _entry.id 6P6D # _exptl.entry_id 6P6D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 121.158 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description CYSTEINE _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 6P6D _cell.length_a 50.192 _cell.length_b 81.066 _cell.length_c 136.91 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6P6D _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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 _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 ? 3 E N N ? 3 F N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type 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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 2 5 4 NAG MAN C1 O1 . O2 HO2 . sing 5 ? 2 6 3 MAN BMA C1 O1 . O6 HO6 . sing 6 ? 2 7 6 NAG MAN C1 O1 . O2 HO2 . sing 7 ? 2 8 1 FUC NAG C1 O1 . O6 HO6 . 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 2 n C NAG 1 C 1 NAG A 601 NAG 2 n C NAG 2 C 2 NAG A 602 NAG 2 n C BMA 3 C 3 BMA A 603 BMA 2 n C MAN 4 C 4 MAN A 605 MAN 2 n C NAG 5 C 5 NAG A 606 NAG 2 n C MAN 6 C 6 MAN A 607 MAN 2 n C NAG 7 C 7 NAG A 608 NAG 2 n C FUC 8 C 8 FUC A 604 FUC 2 n D NAG 1 D 1 NAG B 601 NAG 2 n D NAG 2 D 2 NAG B 602 NAG 2 n D BMA 3 D 3 BMA B 603 BMA 2 n D MAN 4 D 4 MAN B 605 MAN 2 n D NAG 5 D 5 NAG B 606 NAG 2 n D MAN 6 D 6 MAN B 607 MAN 2 n D NAG 7 D 7 NAG B 608 NAG 2 n D FUC 8 D 8 FUC B 604 FUC # 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 20 A CYS 239 1_555 E SG CYS . A CYS 609 1_555 i ? ? ? ? ? ? ? ? ? ? ? 2.075 ? disulf ? disulf2 A SG CYS 42 A CYS 261 1_555 A SG CYS 102 A CYS 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf3 A SG CYS 148 A CYS 367 1_555 A SG CYS 206 A CYS 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? disulf ? disulf4 B SG CYS 20 B CYS 239 1_555 F SG CYS . B CYS 609 1_555 i ? ? ? ? ? ? ? ? ? ? ? 2.097 ? disulf ? disulf5 B SG CYS 42 B CYS 261 1_555 B SG CYS 102 B CYS 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf6 B SG CYS 148 B CYS 367 1_555 B SG CYS 206 B CYS 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? covale ? covale1 A ND2 ASN 78 A ASN 297 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale2 B ND2 ASN 78 B ASN 297 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale3 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale4 C O6 NAG . C NAG 1 1_555 C C1 FUC . C FUC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale5 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale6 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.482 ? covale ? covale7 C O6 BMA . C BMA 3 1_555 C C1 MAN . C MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.41 ? covale ? covale8 C O2 MAN . C MAN 4 1_555 C C1 NAG . C NAG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale9 C O2 MAN . C MAN 6 1_555 C C1 NAG . C NAG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale10 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.477 ? covale ? covale11 D O6 NAG . D NAG 1 1_555 D C1 FUC . D FUC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale12 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale13 D O3 BMA . D BMA 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale14 D O6 BMA . D BMA 3 1_555 D C1 MAN . D MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale15 D O2 MAN . D MAN 4 1_555 D C1 NAG . D NAG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.482 ? covale ? covale16 D O2 MAN . D MAN 6 1_555 D C1 NAG . D NAG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? # _chem_comp.formula 'C3 H7 N O2 S' _chem_comp.formula_weight 121.158 _chem_comp.id CYS _chem_comp.mon_nstd_flag y _chem_comp.name CYSTEINE _chem_comp.type 'l-peptide linking' _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 CYS sing 94 n n N H CYS sing 95 n n N H2 CYS sing 96 n n CA C CYS sing 97 n n CA CB CYS sing 98 n n CA HA CYS sing 99 n n C O CYS doub 100 n n C OXT CYS sing 101 n n CB SG CYS sing 102 n n CB HB2 CYS sing 103 n n CB HB3 CYS sing 104 n n SG HG CYS sing 105 n n OXT HXT CYS sing 106 n n # _atom_sites.entry_id 6P6D _atom_sites.fract_transf_matrix[1][1] 0.019923 _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] 0.012336 _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] 0.007304 _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 E 3 CYS A 1 609 501 CYS CYS . F 3 CYS B 1 609 502 CYS CYS . G 4 HOH A 1 701 717 HOH HOH . G 4 HOH A 2 702 736 HOH HOH . G 4 HOH A 3 703 731 HOH HOH . G 4 HOH A 4 704 687 HOH HOH . G 4 HOH A 5 705 704 HOH HOH . G 4 HOH A 6 706 746 HOH HOH . G 4 HOH A 7 707 727 HOH HOH . G 4 HOH A 8 708 668 HOH HOH . G 4 HOH A 9 709 680 HOH HOH . G 4 HOH A 10 710 716 HOH HOH . G 4 HOH A 11 711 690 HOH HOH . G 4 HOH A 12 712 689 HOH HOH . G 4 HOH A 13 713 730 HOH HOH . G 4 HOH A 14 714 726 HOH HOH . G 4 HOH A 15 715 714 HOH HOH . G 4 HOH A 16 716 683 HOH HOH . G 4 HOH A 17 717 653 HOH HOH . G 4 HOH A 18 718 684 HOH HOH . G 4 HOH A 19 719 725 HOH HOH . G 4 HOH A 20 720 713 HOH HOH . G 4 HOH A 21 721 660 HOH HOH . G 4 HOH A 22 722 656 HOH HOH . G 4 HOH A 23 723 710 HOH HOH . G 4 HOH A 24 724 718 HOH HOH . G 4 HOH A 25 725 655 HOH HOH . G 4 HOH A 26 726 721 HOH HOH . G 4 HOH A 27 727 688 HOH HOH . G 4 HOH A 28 728 707 HOH HOH . G 4 HOH A 29 729 719 HOH HOH . G 4 HOH A 30 730 685 HOH HOH . G 4 HOH A 31 731 715 HOH HOH . G 4 HOH A 32 732 686 HOH HOH . G 4 HOH A 33 733 695 HOH HOH . G 4 HOH A 34 734 722 HOH HOH . G 4 HOH A 35 735 729 HOH HOH . G 4 HOH A 36 736 694 HOH HOH . G 4 HOH A 37 737 651 HOH HOH . G 4 HOH A 38 738 720 HOH HOH . G 4 HOH A 39 739 724 HOH HOH . G 4 HOH A 40 740 711 HOH HOH . G 4 HOH A 41 741 732 HOH HOH . G 4 HOH A 42 742 712 HOH HOH . G 4 HOH A 43 743 745 HOH HOH . G 4 HOH A 44 744 676 HOH HOH . G 4 HOH A 45 745 671 HOH HOH . G 4 HOH A 46 746 679 HOH HOH . G 4 HOH A 47 747 728 HOH HOH . G 4 HOH A 48 748 708 HOH HOH . G 4 HOH A 49 749 744 HOH HOH . G 4 HOH A 50 750 723 HOH HOH . G 4 HOH A 51 751 756 HOH HOH . G 4 HOH A 52 752 748 HOH HOH . G 4 HOH A 53 753 663 HOH HOH . G 4 HOH A 54 754 670 HOH HOH . G 4 HOH A 55 755 664 HOH HOH . H 4 HOH B 1 701 657 HOH HOH . H 4 HOH B 2 702 734 HOH HOH . H 4 HOH B 3 703 733 HOH HOH . H 4 HOH B 4 704 749 HOH HOH . H 4 HOH B 5 705 751 HOH HOH . H 4 HOH B 6 706 696 HOH HOH . H 4 HOH B 7 707 755 HOH HOH . H 4 HOH B 8 708 754 HOH HOH . H 4 HOH B 9 709 652 HOH HOH . H 4 HOH B 10 710 737 HOH HOH . H 4 HOH B 11 711 697 HOH HOH . H 4 HOH B 12 712 753 HOH HOH . H 4 HOH B 13 713 693 HOH HOH . H 4 HOH B 14 714 703 HOH HOH . H 4 HOH B 15 715 658 HOH HOH . H 4 HOH B 16 716 752 HOH HOH . H 4 HOH B 17 717 738 HOH HOH . H 4 HOH B 18 718 705 HOH HOH . H 4 HOH B 19 719 735 HOH HOH . H 4 HOH B 20 720 700 HOH HOH . H 4 HOH B 21 721 666 HOH HOH . H 4 HOH B 22 722 691 HOH HOH . H 4 HOH B 23 723 709 HOH HOH . H 4 HOH B 24 724 742 HOH HOH . H 4 HOH B 25 725 698 HOH HOH . H 4 HOH B 26 726 678 HOH HOH . H 4 HOH B 27 727 741 HOH HOH . H 4 HOH B 28 728 743 HOH HOH . H 4 HOH B 29 729 702 HOH HOH . H 4 HOH B 30 730 701 HOH HOH . H 4 HOH B 31 731 750 HOH HOH . H 4 HOH B 32 732 739 HOH HOH . H 4 HOH B 33 733 669 HOH HOH . H 4 HOH B 34 734 706 HOH HOH . H 4 HOH B 35 735 699 HOH HOH . H 4 HOH B 36 736 681 HOH HOH . H 4 HOH B 37 737 692 HOH HOH . H 4 HOH B 38 738 682 HOH HOH . H 4 HOH B 39 739 672 HOH HOH . H 4 HOH B 40 740 740 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 N N CYS . . . E 3 -4.532 -5.56 63.116 1 57.43 ? N CYS 609 A 1 HETATM 2 C CA CYS . . . E 3 -5.05 -5.891 64.49 1 55.99 ? CA CYS 609 A 1 HETATM 3 C C CYS . . . E 3 -3.893 -5.862 65.499 1 65.24 ? C CYS 609 A 1 HETATM 4 O O CYS . . . E 3 -2.895 -6.63 65.28 1 60.15 ? O CYS 609 A 1 HETATM 5 C CB CYS . . . E 3 -5.685 -7.282 64.448 1 56.64 ? CB CYS 609 A 1 HETATM 6 S SG CYS . . . E 3 -6.791 -7.618 65.869 1 56.69 ? SG CYS 609 A 1 HETATM 7 O OXT CYS . . . E 3 -3.899 -5.107 66.528 1 58.35 -1 OXT CYS 609 A 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 260 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 7 #