data_6Y9M # _model_server_result.job_id vR1jsU-mTVXUZzRnDBid6w _model_server_result.datetime_utc '2025-02-28 15:05:50' _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 6y9m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":508}' # _entry.id 6Y9M # _exptl.entry_id 6Y9M _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 94.971 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'PHOSPHATE ION' _entity.pdbx_number_of_molecules 5 _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 6Y9M _cell.length_a 167.2 _cell.length_b 218.2 _cell.length_c 145.5 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6Y9M _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 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 PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_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,D,E,F,K,L,M,N,S 1 1 B,C,G,H,I,J,O,P,Q,R,T,U 2 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 ? 5 M N N ? 5 N N N ? 5 O N N ? 5 P N N ? 5 R N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 3 4 1 FUC NAG C1 O1 . O6 HO6 . sing 5 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 6 ? 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 2 n E NAG 1 E 1 NAG A 501 NAG 2 n E NAG 2 E 2 NAG A 502 NAG 2 n F NAG 1 F 1 NAG A 505 NAG 2 n F NAG 2 F 2 NAG A 506 NAG 3 n G NAG 1 G 1 NAG B 501 NAG 3 n G NAG 2 G 2 NAG B 502 NAG 3 n G BMA 3 G 3 BMA B 503 BMA 3 n G FUC 4 G 4 FUC B 504 FUC 2 n H NAG 1 H 1 NAG B 507 NAG 2 n H NAG 2 H 2 NAG B 508 NAG 2 n I NAG 1 I 1 NAG C 501 NAG 2 n I NAG 2 I 2 NAG C 502 NAG 4 n J NAG 1 J 1 NAG C 504 NAG 4 n J NAG 2 J 2 NAG C 505 NAG 4 n J BMA 3 J 3 BMA C 506 BMA 2 n K NAG 1 K 1 NAG D 501 NAG 2 n K NAG 2 K 2 NAG D 502 NAG 2 n L NAG 1 L 1 NAG D 503 NAG 2 n L NAG 2 L 2 NAG D 504 NAG # 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 79 A CYS 114 1_555 A SG CYS 110 A CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? disulf ? disulf2 A SG CYS 87 A CYS 122 1_555 A SG CYS 121 A CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? disulf ? disulf3 A SG CYS 189 A CYS 224 1_555 A SG CYS 250 A CYS 285 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf4 B SG CYS 79 B CYS 114 1_555 B SG CYS 110 B CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? disulf ? disulf5 B SG CYS 87 B CYS 122 1_555 B SG CYS 121 B CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? disulf ? disulf6 B SG CYS 189 B CYS 224 1_555 B SG CYS 250 B CYS 285 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf7 B SG CYS 267 B CYS 302 1_555 D SG CYS 267 D CYS 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? disulf ? disulf8 C SG CYS 79 C CYS 114 1_555 C SG CYS 110 C CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? disulf ? disulf9 C SG CYS 87 C CYS 122 1_555 C SG CYS 121 C CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? disulf ? disulf10 C SG CYS 189 C CYS 224 1_555 C SG CYS 250 C CYS 285 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? disulf ? disulf11 D SG CYS 79 D CYS 114 1_555 D SG CYS 110 D CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? disulf ? disulf12 D SG CYS 87 D CYS 122 1_555 D SG CYS 121 D CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf13 D SG CYS 189 D CYS 224 1_555 D SG CYS 250 D CYS 285 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? covale ? covale1 A ND2 ASN 81 A ASN 116 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale2 A ND2 ASN 175 A ASN 210 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale3 B ND2 ASN 81 B ASN 116 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale4 B ND2 ASN 175 B ASN 210 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale5 C ND2 ASN 81 C ASN 116 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale6 D ND2 ASN 81 D ASN 116 1_555 K C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? covale ? covale7 D ND2 ASN 175 D ASN 210 1_555 L C1 NAG . L NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.479 ? covale ? covale8 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale9 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale10 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale11 G O6 NAG . G NAG 1 1_555 G C1 FUC . G FUC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale12 G O4 NAG . G NAG 2 1_555 G C1 BMA . G BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale13 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale14 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale15 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.471 ? covale ? covale16 J O4 NAG . J NAG 2 1_555 J C1 BMA . J BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale17 K O4 NAG . K NAG 1 1_555 K C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale18 L O4 NAG . L NAG 1 1_555 L C1 NAG . L NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? # _chem_comp.formula 'O4 P -3' _chem_comp.formula_weight 94.971 _chem_comp.id PO4 _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHATE ION' _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 P O1 PO4 doub 337 n n P O2 PO4 sing 338 n n P O3 PO4 sing 339 n n P O4 PO4 sing 340 n n # _atom_sites.entry_id 6Y9M _atom_sites.fract_transf_matrix[1][1] 0.005981 _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] 0.004583 _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] 0.006873 _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 M 5 PO4 A 1 505 510 PO4 PO4 . N 5 PO4 A 1 506 512 PO4 PO4 . O 5 PO4 B 1 507 510 PO4 PO4 . P 5 PO4 B 1 508 512 PO4 PO4 . Q 6 SO4 C 1 506 510 SO4 SO4 . R 5 PO4 C 1 507 511 PO4 PO4 . S 7 HOH A 1 601 1 HOH HOH . S 7 HOH A 2 602 2 HOH HOH . S 7 HOH A 3 603 4 HOH HOH . S 7 HOH A 4 604 8 HOH HOH . S 7 HOH A 5 605 3 HOH HOH . T 7 HOH B 1 601 5 HOH HOH . U 7 HOH C 1 601 6 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 P P PO4 . . . P 5 134.198 95.729 73.382 1 199.99 ? P PO4 508 B 1 HETATM 2 O O1 PO4 . . . P 5 134.392 96.974 72.544 1 185.56 ? O1 PO4 508 B 1 HETATM 3 O O2 PO4 . . . P 5 133.233 94.805 72.66 1 167.69 ? O2 PO4 508 B 1 HETATM 4 O O3 PO4 . . . P 5 135.539 95.065 73.597 1 182.41 ? O3 PO4 508 B 1 HETATM 5 O O4 PO4 . . . P 5 133.677 96.172 74.726 1 231.84 ? O4 PO4 508 B 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 5 #