data_6N2O # _model_server_result.job_id eM9n7qeiIrLnr7w3k-uNvQ _model_server_result.datetime_utc '2025-01-25 11:34:20' _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 6n2o # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":601}' # _entry.id 6N2O # _exptl.entry_id 6N2O _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 867.607 _entity.id 8 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SUCCINYL-COENZYME A' _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 _cell.angle_gamma 90 _cell.entry_id 6N2O _cell.length_a 86.407 _cell.length_b 100.532 _cell.length_c 202.053 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6N2O _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,L,M,N,O,P,Q _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 8 _struct_asym.id J _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 J CS1 SCA . C SCA 601 1_555 L C2 TPP . D TPP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.595 ? metalc ? metalc1 B SG CYS 26 B CYS 26 1_555 G FE4 SF4 . B SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc2 B SG CYS 29 B CYS 29 1_555 G FE2 SF4 . B SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc3 B SG CYS 60 B CYS 60 1_555 G FE3 SF4 . B SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc4 B OD1 ASP 102 B ASP 102 1_555 I MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc5 B OD1 ASN 130 B ASN 130 1_555 I MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc6 B O ILE 132 B ILE 132 1_555 I MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc7 B SG CYS 209 B CYS 209 1_555 G FE1 SF4 . B SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? metalc ? metalc8 H O2A TPP . B TPP 402 1_555 I MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? metalc ? metalc9 H O1B TPP . B TPP 402 1_555 I MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc10 I MG MG . B MG 403 1_555 O O HOH . B HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc11 D SG CYS 26 D CYS 26 1_555 K FE4 SF4 . D SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc12 D SG CYS 29 D CYS 29 1_555 K FE2 SF4 . D SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc13 D SG CYS 60 D CYS 60 1_555 K FE3 SF4 . D SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc14 D OD1 ASP 102 D ASP 102 1_555 M MG MG . D MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc15 D OD1 ASN 130 D ASN 130 1_555 M MG MG . D MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc16 D O ILE 132 D ILE 132 1_555 M MG MG . D MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? metalc ? metalc17 D SG CYS 209 D CYS 209 1_555 K FE1 SF4 . D SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc18 L O1A TPP . D TPP 402 1_555 M MG MG . D MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc19 L O1B TPP . D TPP 402 1_555 M MG MG . D MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc20 M MG MG . D MG 403 1_555 Q O HOH . D HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? # _chem_comp.formula 'C25 H40 N7 O19 P3 S' _chem_comp.formula_weight 867.607 _chem_comp.id SCA _chem_comp.mon_nstd_flag . _chem_comp.name 'SUCCINYL-COENZYME A' _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 C8 N9 SCA sing 378 n y C8 N7 SCA doub 379 n y C8 H8 SCA sing 380 n n N9 C4 SCA sing 381 n y N9 C1' SCA sing 382 n n C4 C5 SCA sing 383 n y C4 N3 SCA doub 384 n y C5 N7 SCA sing 385 n y C5 C6 SCA doub 386 n y N3 C2 SCA sing 387 n y C2 N1 SCA doub 388 n y C2 H2 SCA sing 389 n n N1 C6 SCA sing 390 n y C6 N6 SCA sing 391 n n N6 HN61 SCA sing 392 n n N6 HN62 SCA sing 393 n n C1' C2' SCA sing 394 n n C1' O4' SCA sing 395 n n C1' H1' SCA sing 396 n n C2' O2' SCA sing 397 n n C2' C3' SCA sing 398 n n C2' H2' SCA sing 399 n n O2' HO2' SCA sing 400 n n C3' O3' SCA sing 401 n n C3' C4' SCA sing 402 n n C3' H3' SCA sing 403 n n O3' P3 SCA sing 404 n n C4' O4' SCA sing 405 n n C4' C5' SCA sing 406 n n C4' H4' SCA sing 407 n n C5' O5' SCA sing 408 n n C5' "H5'1" SCA sing 409 n n C5' "H5'2" SCA sing 410 n n O5' P1 SCA sing 411 n n P1 O11 SCA sing 412 n n P1 O12 SCA doub 413 n n P1 O6 SCA sing 414 n n O11 HOB SCA sing 415 n n O6 P2 SCA sing 416 n n P2 O21 SCA doub 417 n n P2 O22 SCA sing 418 n n P2 O7 SCA sing 419 n n O22 HOM SCA sing 420 n n O7 CPB SCA sing 421 n n CPB CPA SCA sing 422 n n CPB HPB1 SCA sing 423 n n CPB HPB2 SCA sing 424 n n CPA CP7 SCA sing 425 n n CPA CP9 SCA sing 426 n n CPA CP8 SCA sing 427 n n CP7 OP3 SCA sing 428 n n CP7 CP6 SCA sing 429 n n CP7 H7 SCA sing 430 n n CP9 H91 SCA sing 431 n n CP9 H92 SCA sing 432 n n CP9 H93 SCA sing 433 n n CP8 H81 SCA sing 434 n n CP8 H82 SCA sing 435 n n CP8 H83 SCA sing 436 n n OP3 HO3 SCA sing 437 n n CP6 OP2 SCA doub 438 n n CP6 NP2 SCA sing 439 n n NP2 CP5 SCA sing 440 n n NP2 HN2 SCA sing 441 n n CP5 CP4 SCA sing 442 n n CP5 H51 SCA sing 443 n n CP5 H52 SCA sing 444 n n CP4 CP3 SCA sing 445 n n CP4 H41 SCA sing 446 n n CP4 H42 SCA sing 447 n n CP3 OP1 SCA doub 448 n n CP3 NP1 SCA sing 449 n n NP1 CP2 SCA sing 450 n n NP1 HN1 SCA sing 451 n n CP2 CP1 SCA sing 452 n n CP2 H21 SCA sing 453 n n CP2 H22 SCA sing 454 n n CP1 S SCA sing 455 n n CP1 H11 SCA sing 456 n n CP1 H12 SCA sing 457 n n P3 O31 SCA doub 458 n n P3 O32 SCA sing 459 n n P3 O33 SCA sing 460 n n O32 HOW SCA sing 461 n n O33 HOX SCA sing 462 n n S CS1 SCA sing 463 n n CS1 OS1 SCA doub 464 n n CS1 CS2 SCA sing 465 n n CS2 CS3 SCA sing 466 n n CS2 HS21 SCA sing 467 n n CS2 HS22 SCA sing 468 n n CS3 CS4 SCA sing 469 n n CS3 HS31 SCA sing 470 n n CS3 HS32 SCA sing 471 n n CS4 OS4 SCA sing 472 n n CS4 OS5 SCA doub 473 n n OS4 HO4 SCA sing 474 n n # _atom_sites.entry_id 6N2O _atom_sites.fract_transf_matrix[1][1] 0.011573 _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] 0.009947 _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] 0.004949 _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 AKG A 1 601 4 AKG AKG . F 4 COA A 1 602 5 COA COA . G 5 SF4 B 1 401 401 SF4 SF4 . H 6 TPP B 1 402 402 TPP TPP . I 7 MG B 1 403 403 MG MG . J 8 SCA C 1 601 3 SCA SCA . K 5 SF4 D 1 401 401 SF4 SF4 . L 6 TPP D 1 402 402 TPP TPP . M 7 MG D 1 403 403 MG MG . N 9 HOH A 1 701 5 HOH HOH . N 9 HOH A 2 702 3 HOH HOH . N 9 HOH A 3 703 7 HOH HOH . N 9 HOH A 4 704 4 HOH HOH . N 9 HOH A 5 705 11 HOH HOH . N 9 HOH A 6 706 13 HOH HOH . N 9 HOH A 7 707 16 HOH HOH . N 9 HOH A 8 708 12 HOH HOH . O 9 HOH B 1 501 15 HOH HOH . O 9 HOH B 2 502 8 HOH HOH . O 9 HOH B 3 503 10 HOH HOH . O 9 HOH B 4 504 1 HOH HOH . O 9 HOH B 5 505 6 HOH HOH . O 9 HOH B 6 506 17 HOH HOH . P 9 HOH C 1 701 14 HOH HOH . P 9 HOH C 2 702 18 HOH HOH . P 9 HOH C 3 703 9 HOH HOH . P 9 HOH C 4 704 20 HOH HOH . P 9 HOH C 5 705 1 HOH HOH . P 9 HOH C 6 706 19 HOH HOH . Q 9 HOH D 1 501 2 HOH HOH . Q 9 HOH D 2 502 2 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 C8 SCA . . . J 8 -8.221 -2.927 -52.116 1 86.91 ? C8 SCA 601 C 1 HETATM 2 N N9 SCA . . . J 8 -7.117 -2.071 -52.513 1 88.94 ? N9 SCA 601 C 1 HETATM 3 C C4 SCA . . . J 8 -7.448 -1.622 -53.781 1 90.11 ? C4 SCA 601 C 1 HETATM 4 C C5 SCA . . . J 8 -8.65 -2.157 -54.167 1 89.88 ? C5 SCA 601 C 1 HETATM 5 N N7 SCA . . . J 8 -9.105 -2.943 -53.149 1 89.85 ? N7 SCA 601 C 1 HETATM 6 N N3 SCA . . . J 8 -6.737 -0.787 -54.593 1 90.11 ? N3 SCA 601 C 1 HETATM 7 C C2 SCA . . . J 8 -7.251 -0.49 -55.797 1 89.5 ? C2 SCA 601 C 1 HETATM 8 N N1 SCA . . . J 8 -8.431 -0.998 -56.202 1 89.9 ? N1 SCA 601 C 1 HETATM 9 C C6 SCA . . . J 8 -9.147 -1.833 -55.41 1 88.47 ? C6 SCA 601 C 1 HETATM 10 N N6 SCA . . . J 8 -10.334 -2.34 -55.821 1 88.58 ? N6 SCA 601 C 1 HETATM 11 C C1' SCA . . . J 8 -6.297 -1.406 -51.505 1 89.71 ? C1' SCA 601 C 1 HETATM 12 C C2' SCA . . . J 8 -7.155 -0.708 -50.451 1 87.32 ? C2' SCA 601 C 1 HETATM 13 O O2' SCA . . . J 8 -7.451 0.655 -50.78 1 84.12 ? O2' SCA 601 C 1 HETATM 14 C C3' SCA . . . J 8 -6.328 -0.821 -49.198 1 87.26 ? C3' SCA 601 C 1 HETATM 15 O O3' SCA . . . J 8 -5.252 0.104 -49.325 1 90.95 ? O3' SCA 601 C 1 HETATM 16 C C4' SCA . . . J 8 -5.721 -2.196 -49.38 1 87.72 ? C4' SCA 601 C 1 HETATM 17 O O4' SCA . . . J 8 -5.408 -2.247 -50.779 1 92.49 ? O4' SCA 601 C 1 HETATM 18 C C5' SCA . . . J 8 -6.655 -3.345 -49.042 1 84.85 ? C5' SCA 601 C 1 HETATM 19 O O5' SCA . . . J 8 -7.114 -3.187 -47.707 1 84.83 ? O5' SCA 601 C 1 HETATM 20 P P1 SCA . . . J 8 -8.658 -2.854 -47.425 1 83.07 ? P1 SCA 601 C 1 HETATM 21 O O11 SCA . . . J 8 -8.747 -1.872 -46.291 1 83.2 ? O11 SCA 601 C 1 HETATM 22 O O12 SCA . . . J 8 -9.307 -2.488 -48.728 1 83.65 ? O12 SCA 601 C 1 HETATM 23 O O6 SCA . . . J 8 -9.307 -4.25 -46.945 1 80.58 ? O6 SCA 601 C 1 HETATM 24 P P2 SCA . . . J 8 -8.704 -5.747 -46.843 1 79.71 ? P2 SCA 601 C 1 HETATM 25 O O21 SCA . . . J 8 -8.137 -6.128 -48.182 1 83.91 ? O21 SCA 601 C 1 HETATM 26 O O22 SCA . . . J 8 -9.681 -6.655 -46.15 1 78.62 ? O22 SCA 601 C 1 HETATM 27 O O7 SCA . . . J 8 -7.442 -5.399 -45.765 1 79.71 ? O7 SCA 601 C 1 HETATM 28 C CPB SCA . . . J 8 -7.109 -6.31 -44.714 1 78.47 ? CPB SCA 601 C 1 HETATM 29 C CPA SCA . . . J 8 -6.41 -5.509 -43.623 1 77.07 ? CPA SCA 601 C 1 HETATM 30 C CP7 SCA . . . J 8 -6.137 -6.357 -42.368 1 79.91 ? CP7 SCA 601 C 1 HETATM 31 C CP9 SCA . . . J 8 -7.253 -4.286 -43.305 1 80.47 ? CP9 SCA 601 C 1 HETATM 32 C CP8 SCA . . . J 8 -5.14 -4.843 -44.13 1 75.29 ? CP8 SCA 601 C 1 HETATM 33 O OP3 SCA . . . J 8 -5.369 -7.533 -42.716 1 81.26 ? OP3 SCA 601 C 1 HETATM 34 C CP6 SCA . . . J 8 -5.564 -5.614 -41.175 1 79.41 ? CP6 SCA 601 C 1 HETATM 35 O OP2 SCA . . . J 8 -6.289 -4.917 -40.48 1 81.04 ? OP2 SCA 601 C 1 HETATM 36 N NP2 SCA . . . J 8 -4.271 -5.757 -40.898 1 77.47 ? NP2 SCA 601 C 1 HETATM 37 C CP5 SCA . . . J 8 -3.576 -5.103 -39.785 1 73.86 ? CP5 SCA 601 C 1 HETATM 38 C CP4 SCA . . . J 8 -3.711 -5.818 -38.437 1 71.02 ? CP4 SCA 601 C 1 HETATM 39 C CP3 SCA . . . J 8 -3.219 -4.887 -37.346 1 66.86 ? CP3 SCA 601 C 1 HETATM 40 O OP1 SCA . . . J 8 -3.847 -3.868 -37.082 1 68.17 ? OP1 SCA 601 C 1 HETATM 41 N NP1 SCA . . . J 8 -2.093 -5.185 -36.686 1 62.96 ? NP1 SCA 601 C 1 HETATM 42 C CP2 SCA . . . J 8 -1.47 -4.399 -35.617 1 60.39 ? CP2 SCA 601 C 1 HETATM 43 C CP1 SCA . . . J 8 -1.103 -5.242 -34.398 1 62.29 ? CP1 SCA 601 C 1 HETATM 44 P P3 SCA . . . J 8 -4.68 1.033 -48.143 1 92.98 ? P3 SCA 601 C 1 HETATM 45 O O31 SCA . . . J 8 -4.823 2.441 -48.676 1 83.84 ? O31 SCA 601 C 1 HETATM 46 O O32 SCA . . . J 8 -3.248 0.589 -47.956 1 83.59 ? O32 SCA 601 C 1 HETATM 47 O O33 SCA . . . J 8 -5.561 0.732 -46.953 1 86.92 ? O33 SCA 601 C 1 HETATM 48 S S SCA . . . J 8 -0.489 -4.197 -33.039 1 63.87 ? S SCA 601 C 1 HETATM 49 C CS1 SCA . . . J 8 1.089 -4.763 -32.484 1 59.34 ? CS1 SCA 601 C 1 HETATM 50 O OS1 SCA . . . J 8 0.959 -5.135 -31.096 1 56.63 ? OS1 SCA 601 C 1 HETATM 51 C CS2 SCA . . . J 8 1.45 -5.996 -33.269 1 59.98 ? CS2 SCA 601 C 1 HETATM 52 C CS3 SCA . . . J 8 1.374 -7.271 -32.439 1 58.76 ? CS3 SCA 601 C 1 HETATM 53 C CS4 SCA . . . J 8 1.734 -8.516 -33.203 1 59.59 ? CS4 SCA 601 C 1 HETATM 54 O OS4 SCA . . . J 8 2.882 -8.886 -33.386 1 56.52 ? OS4 SCA 601 C 1 HETATM 55 O OS5 SCA . . . J 8 0.689 -9.171 -33.647 1 58.1 ? OS5 SCA 601 C 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 55 #