data_2GD4 # _model_server_result.job_id 1W7W6OWAy4C3I6_lA0ppDQ _model_server_result.datetime_utc '2024-11-22 22:24:18' _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 2gd4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":401}' # _entry.id 2GD4 # _exptl.entry_id 2GD4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 40.078 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'CALCIUM ION' _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 113.14 _cell.angle_gamma 90 _cell.entry_id 2GD4 _cell.length_a 220.263 _cell.length_b 60.588 _cell.length_c 156.174 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GD4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # 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 trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 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,B,C,G,I,K,L,M,Q,R,S 1 1 D,E,F,H,J,N,O,P,T,U,V 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 ? 7 K N N ? 7 N N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 4 oligosaccharide 5 oligosaccharide 6 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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 4 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 4 5 4 MAN MAN C1 O1 . O2 HO2 . sing 5 ? 4 6 3 MAN BMA C1 O1 . O6 HO6 . sing 6 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 7 ? 6 2 1 IDS ZDO C1 O1 . O4 HO4 . sing 8 ? 6 3 2 SUS IDS C1 O1 . O4 HO4 . sing 9 ? 6 4 3 BDP SUS C1 O1 . O4 HO4 . sing 10 ? 6 5 4 SGN BDP 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 4 n G NAG 1 D 1 NAG I 601 NAG 4 n G NAG 2 D 2 NAG I 602 NAG 4 n G BMA 3 D 3 BMA I 603 BMA 4 n G MAN 4 D 4 MAN I 605 MAN 4 n G MAN 5 D 5 MAN I 606 MAN 4 n G MAN 6 D 6 MAN I 604 MAN 5 n H NAG 1 E 1 NAG C 601 NAG 5 n H NAG 2 E 2 NAG C 602 NAG 6 n I ZDO 1 F 1 ZDO ? 901 NTO 6 n I IDS 2 F 2 IDS ? 901 NTO 6 n I SUS 3 F 3 SUS ? 901 NTO 6 n I BDP 4 F 4 BDP ? 901 NTO 6 n I SGN 5 F 5 SGN ? 901 NTO 6 n J ZDO 1 G 1 ZDO ? 902 NTO 6 n J IDS 2 G 2 IDS ? 902 NTO 6 n J SUS 3 G 3 SUS ? 902 NTO 6 n J BDP 4 G 4 BDP ? 902 NTO 6 n J SGN 5 G 5 SGN ? 902 NTO # 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 L CYS 89 1_555 A SG CYS 16 L CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 12 L CYS 96 1_555 A SG CYS 25 L CYS 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf3 A SG CYS 27 L CYS 111 1_555 A SG CYS 40 L CYS 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 A SG CYS 48 L CYS 132 1_555 B SG CYS 108 H CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf5 B SG CYS 7 H CYS 22 1_555 B SG CYS 12 H CYS 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf6 B SG CYS 27 H CYS 42 1_555 B SG CYS 43 H CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf7 B SG CYS 156 H CYS 168 1_555 B SG CYS 170 H CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 B SG CYS 181 H CYS 191 1_555 B SG CYS 209 H CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf9 C SG CYS 19 I CYS 8 1_555 C SG CYS 139 I CYS 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf10 C SG CYS 32 I CYS 21 1_555 C SG CYS 106 I CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf11 C SG CYS 258 I CYS 247 1_555 C SG CYS 441 I CYS 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf12 D SG CYS 5 A CYS 89 1_555 D SG CYS 16 A CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf13 D SG CYS 12 A CYS 96 1_555 D SG CYS 25 A CYS 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf14 D SG CYS 27 A CYS 111 1_555 D SG CYS 40 A CYS 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf15 D SG CYS 48 A CYS 132 1_555 E SG CYS 108 B CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf16 E SG CYS 7 B CYS 22 1_555 E SG CYS 12 B CYS 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf17 E SG CYS 27 B CYS 42 1_555 E SG CYS 43 B CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf18 E SG CYS 156 B CYS 168 1_555 E SG CYS 170 B CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf19 E SG CYS 181 B CYS 191 1_555 E SG CYS 209 B CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf20 F SG CYS 19 C CYS 8 1_555 F SG CYS 139 C CYS 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf21 F SG CYS 32 C CYS 21 1_555 F SG CYS 106 C CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf22 F SG CYS 258 C CYS 247 1_555 F SG CYS 441 C CYS 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? covale ? covale1 C ND2 ASN 107 I ASN 96 1_555 L C1 NAG . I NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? covale ? covale2 C ND2 ASN 166 I ASN 155 1_555 G C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale3 C ND2 ASN 203 I ASN 192 1_555 M C1 NAG . I NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale4 F ND2 ASN 107 C ASN 96 1_555 O C1 NAG . C NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale5 F ND2 ASN 166 C ASN 155 1_555 H C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale6 F ND2 ASN 203 C ASN 192 1_555 P C1 NAG . C NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale7 G O4 NAG . D NAG 1 1_555 G C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? covale ? covale8 G O4 NAG . D NAG 2 1_555 G C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.396 ? covale ? covale9 G O3 BMA . D BMA 3 1_555 G C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.404 ? covale ? covale10 G O6 BMA . D BMA 3 1_555 G C1 MAN . D MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.406 ? covale ? covale11 G O2 MAN . D MAN 4 1_555 G C1 MAN . D MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.402 ? covale ? covale12 H O4 NAG . E NAG 1 1_555 H C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? covale ? covale13 I O4 ZDO . F ZDO 1 1_555 I C1 IDS . F IDS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 sing covale ? covale14 I O4 IDS . F IDS 2 1_555 I C1 SUS . F SUS 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 sing covale ? covale15 I O4 SUS . F SUS 3 1_555 I C1 BDP . F BDP 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 sing covale ? covale16 I O4 BDP . F BDP 4 1_555 I C1 SGN . F SGN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 sing covale ? covale17 J O4 ZDO . G ZDO 1 1_555 J C1 IDS . G IDS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 sing covale ? covale18 J O4 IDS . G IDS 2 1_555 J C1 SUS . G SUS 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 sing covale ? covale19 J O4 SUS . G SUS 3 1_555 J C1 BDP . G BDP 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 sing covale ? covale20 J O4 BDP . G BDP 4 1_555 J C1 SGN . G SGN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 sing metalc ? metalc1 B OD1 ASP 56 H ASP 70 1_555 K CA CA . H CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc2 B O ASN 58 H ASN 72 1_555 K CA CA . H CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.896 ? metalc ? metalc3 B O GLN 61 H GLN 75 1_555 K CA CA . H CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.779 ? metalc ? metalc4 B OE1 GLU 63 H GLU 77 1_555 K CA CA . H CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.906 ? metalc ? metalc5 B OE1 GLU 66 H GLU 80 1_555 K CA CA . H CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc6 K CA CA . H CA 401 1_555 R O HOH . H HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? metalc ? metalc7 E OD1 ASP 56 B ASP 70 1_555 N CA CA . B CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.437 ? metalc ? metalc8 E O ASN 58 B ASN 72 1_555 N CA CA . B CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc9 E O GLN 61 B GLN 75 1_555 N CA CA . B CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc10 E OE1 GLU 66 B GLU 80 1_555 N CA CA . B CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc11 E OE2 GLU 66 B GLU 80 1_555 N CA CA . B CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? # _chem_comp.formula 'Ca 2' _chem_comp.formula_weight 40.078 _chem_comp.id CA _chem_comp.mon_nstd_flag . _chem_comp.name 'CALCIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 2GD4 _atom_sites.fract_transf_matrix[1][1] 0.00454 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00194 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016505 _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] 0.006963 _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 7 CA H 1 401 401 CA CA . L 8 NAG I 1 501 501 NAG NAG . M 8 NAG I 1 701 701 NAG NAG . N 7 CA B 1 401 401 CA CA . O 8 NAG C 1 501 501 NAG NAG . P 8 NAG C 1 701 701 NAG NAG . Q 9 HOH L 1 6 6 HOH HOH . Q 9 HOH L 2 38 38 HOH HOH . Q 9 HOH L 3 43 43 HOH HOH . R 9 HOH H 1 402 1 HOH HOH . R 9 HOH H 2 403 5 HOH HOH . R 9 HOH H 3 404 7 HOH HOH . R 9 HOH H 4 405 8 HOH HOH . R 9 HOH H 5 406 39 HOH HOH . R 9 HOH H 6 407 40 HOH HOH . R 9 HOH H 7 408 41 HOH HOH . R 9 HOH H 8 409 42 HOH HOH . R 9 HOH H 9 410 44 HOH HOH . R 9 HOH H 10 411 45 HOH HOH . S 9 HOH I 1 902 2 HOH HOH . S 9 HOH I 2 903 3 HOH HOH . S 9 HOH I 3 904 9 HOH HOH . S 9 HOH I 4 905 10 HOH HOH . S 9 HOH I 5 906 11 HOH HOH . S 9 HOH I 6 907 12 HOH HOH . S 9 HOH I 7 908 13 HOH HOH . S 9 HOH I 8 909 14 HOH HOH . S 9 HOH I 9 910 15 HOH HOH . S 9 HOH I 10 911 16 HOH HOH . S 9 HOH I 11 912 17 HOH HOH . S 9 HOH I 12 913 18 HOH HOH . S 9 HOH I 13 914 19 HOH HOH . S 9 HOH I 14 915 20 HOH HOH . S 9 HOH I 15 916 35 HOH HOH . S 9 HOH I 16 917 36 HOH HOH . S 9 HOH I 17 918 37 HOH HOH . S 9 HOH I 18 919 46 HOH HOH . S 9 HOH I 19 920 47 HOH HOH . S 9 HOH I 20 921 48 HOH HOH . S 9 HOH I 21 922 49 HOH HOH . S 9 HOH I 22 923 63 HOH HOH . T 9 HOH A 1 27 27 HOH HOH . T 9 HOH A 2 50 50 HOH HOH . U 9 HOH B 1 402 21 HOH HOH . U 9 HOH B 2 403 22 HOH HOH . U 9 HOH B 3 404 23 HOH HOH . U 9 HOH B 4 405 24 HOH HOH . U 9 HOH B 5 406 25 HOH HOH . U 9 HOH B 6 407 26 HOH HOH . U 9 HOH B 7 408 51 HOH HOH . U 9 HOH B 8 409 52 HOH HOH . U 9 HOH B 9 410 53 HOH HOH . V 9 HOH C 1 903 4 HOH HOH . V 9 HOH C 2 904 28 HOH HOH . V 9 HOH C 3 905 29 HOH HOH . V 9 HOH C 4 906 30 HOH HOH . V 9 HOH C 5 907 31 HOH HOH . V 9 HOH C 6 908 32 HOH HOH . V 9 HOH C 7 909 33 HOH HOH . V 9 HOH C 8 910 34 HOH HOH . V 9 HOH C 9 911 54 HOH HOH . V 9 HOH C 10 912 55 HOH HOH . V 9 HOH C 11 913 56 HOH HOH . V 9 HOH C 12 914 57 HOH HOH . V 9 HOH C 13 915 58 HOH HOH . V 9 HOH C 14 916 59 HOH HOH . V 9 HOH C 15 917 60 HOH HOH . V 9 HOH C 16 918 61 HOH HOH . V 9 HOH C 17 919 62 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol CA _atom_site.label_atom_id CA _atom_site.label_comp_id CA _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id K _atom_site.label_entity_id 7 _atom_site.Cartn_x -25.011 _atom_site.Cartn_y -28.233 _atom_site.Cartn_z 53.291 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 19.99 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 401 _atom_site.auth_asym_id H _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 1 #