data_5XTD
#
_model_server_result.job_id            DmVsPjVTKQpaVqZO2daIyA 
_model_server_result.datetime_utc      '2024-10-31 07:18:20' 
_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          5xtd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"RB","auth_seq_id":703}' 
#
_entry.id    5XTD 
#
_exptl.entry_id    5XTD 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              1464.043 
_entity.id                          51 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            CARDIOLIPIN 
_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            5XTD 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               1 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5XTD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    45-meric 
_pdbx_struct_assembly.oligomeric_count      45 
_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,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,JB,KB,LB,MB,NB,OB,PB,QB,RB,SB,TB,UB,VB,WB 
_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    ? 
_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
? 51 GB N N 
? 51 OB N N 
? 51 RB N N 
? 51 SB N N 
? 51 TB N 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
disulf ? disulf1 T SG CYS 94 V CYS 95 1_555 T SG CYS 114 V CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf2 AA SG CYS 111 c CYS 144 1_555 JA SG CYS 279 l CYS 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
disulf ? disulf3 BA SG CYS 149 d CYS 149 1_555 CA SG CYS 88 e CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
disulf ? disulf4 FA SG CYS 32 h CYS 33 1_555 FA SG CYS 65 h CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
disulf ? disulf5 FA SG CYS 42 h CYS 43 1_555 FA SG CYS 55 h CYS 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf6 QA SG CYS 75 u CYS 78 1_555 QA SG CYS 107 u CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? 
disulf ? disulf7 RA SG CYS 69 v CYS 69 1_555 RA SG CYS 80 v CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.94 ? 
metalc ? metalc1 A NE2 GLN 355 A GLN 381 1_555 TA FE1 SF4 . A SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? 
metalc ? metalc2 B N CYS 80 B CYS 114 1_555 VA FE2 SF4 . B SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.665 ? 
metalc ? metalc3 B N GLY 120 B GLY 154 1_555 WA FE4 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.794 ? 
metalc ? metalc4 C SG CYS 32 C CYS 89 1_555 YA FE2 SF4 . C SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.587 ? 
metalc ? metalc5 L NE2 HIS 95 M HIS 124 1_555 BB FE3 SF4 . M SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? 
metalc ? metalc6 L SG CYS 108 M CYS 137 1_555 BB FE4 SF4 . M SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.56 ? 
covale ? covale1 L SG CYS 147 M CYS 176 1_555 CB S3 SF4 . M SF4 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? 
metalc ? metalc7 L SG CYS 147 M CYS 176 1_555 CB FE1 SF4 . M SF4 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? 
metalc ? metalc8 L O CYS 150 M CYS 179 1_555 CB FE1 SF4 . M SF4 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.567 ? 
metalc ? metalc9 N SG CYS 141 O CYS 176 1_555 EB FE2 FES . O FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.516 ? 
metalc ? metalc10 N SG CYS 145 O CYS 180 1_555 EB FE2 FES . O FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? 
#
_chem_comp.formula           'C81 H156 O17 P2 -2' 
_chem_comp.formula_weight    1464.043 
_chem_comp.id                CDL 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              CARDIOLIPIN 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "DIPHOSPHATIDYL GLYCEROL;BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL" 
#
_atom_sites.entry_id                     5XTD 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
TA 45 SF4 A 1 501 501 SF4 SF4 . 
UA 46 FMN A 1 502 502 FMN FMN . 
VA 45 SF4 B 1 301 301 SF4 SF4 . 
WA 45 SF4 B 1 302 302 SF4 SF4 . 
XA 47 PLX B 1 303 401 PLX PLX . 
YA 45 SF4 C 1 301 301 SF4 SF4 . 
ZA 48 8Q1 E 1 201 201 8Q1 8Q1 . 
AB 49 NDP J 1 401 401 NDP NDP . 
BB 45 SF4 M 1 801 801 SF4 SF4 . 
CB 45 SF4 M 1 802 802 SF4 SF4 . 
DB 50 FES M 1 803 803 FES FES . 
EB 50 FES O 1 301 301 FES FES . 
FB 47 PLX U 1 101 101 PLX PLX . 
GB 51 CDL V 1 201 201 CDL CDL . 
HB 52 PEE V 1 202 202 PEE PEE . 
IB 47 PLX V 1 203 203 PLX PLX . 
JB 52 PEE W 1 201 201 PEE PEE . 
KB 47 PLX b 1 201 201 PLX PLX . 
LB 47 PLX g 1 201 201 PLX PLX . 
MB 47 PLX g 1 202 202 PLX PLX . 
NB 47 PLX g 1 203 203 PLX PLX . 
OB 51 CDL i 1 401 401 CDL CDL . 
PB 52 PEE l 1 701 701 PEE PEE . 
QB 52 PEE l 1 702 702 PEE PEE . 
RB 51 CDL l 1 703 703 CDL CDL . 
SB 51 CDL l 1 704 704 CDL CDL . 
TB 51 CDL n 1 101 101 CDL CDL . 
UB 48 8Q1 p 1 201 201 8Q1 8Q1 . 
VB 47 PLX r 1 501 501 PLX PLX . 
WB 47 PLX r 1 502 502 PLX PLX . 
#
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 CDL . . . RB 51 322.168 245.4 252.574 1 29.51 ? C1 CDL 703 l 1 
HETATM 2 O O1 CDL . . . RB 51 321.382 244.478 253.318 1 30.4 ? O1 CDL 703 l 1 
HETATM 3 C CA2 CDL . . . RB 51 323.479 245.625 253.352 1 27.77 ? CA2 CDL 703 l 1 
HETATM 4 O OA2 CDL . . . RB 51 324.486 244.823 252.757 1 29.45 ? OA2 CDL 703 l 1 
HETATM 5 P PA1 CDL . . . RB 51 325.789 245.54 252.214 1 25.06 ? PA1 CDL 703 l 1 
HETATM 6 O OA3 CDL . . . RB 51 325.935 246.919 252.814 1 26.46 ? OA3 CDL 703 l 1 
HETATM 7 O OA4 CDL . . . RB 51 326.967 244.706 252.586 1 26.83 ? OA4 CDL 703 l 1 
HETATM 8 O OA5 CDL . . . RB 51 325.717 245.643 250.631 1 30.32 ? OA5 CDL 703 l 1 
HETATM 9 C CA3 CDL . . . RB 51 326.217 244.508 249.887 1 33.88 ? CA3 CDL 703 l 1 
HETATM 10 C CA4 CDL . . . RB 51 325.061 243.828 249.195 1 37.31 ? CA4 CDL 703 l 1 
HETATM 11 O OA6 CDL . . . RB 51 325.467 243.501 247.866 1 42.51 ? OA6 CDL 703 l 1 
HETATM 12 C CA5 CDL . . . RB 51 325.75 242.092 247.613 1 44.86 ? CA5 CDL 703 l 1 
HETATM 13 O OA7 CDL . . . RB 51 325.865 241.307 248.54 1 47.28 ? OA7 CDL 703 l 1 
HETATM 14 C C11 CDL . . . RB 51 325.896 241.566 246.157 1 43.29 ? C11 CDL 703 l 1 
HETATM 15 C C12 CDL . . . RB 51 324.949 240.404 245.869 1 41.37 ? C12 CDL 703 l 1 
HETATM 16 C C13 CDL . . . RB 51 324.984 240.016 244.386 1 37.64 ? C13 CDL 703 l 1 
HETATM 17 C C14 CDL . . . RB 51 323.739 240.506 243.608 1 36.23 ? C14 CDL 703 l 1 
HETATM 18 C C15 CDL . . . RB 51 323.902 240.323 242.119 1 34.86 ? C15 CDL 703 l 1 
HETATM 19 C C16 CDL . . . RB 51 322.804 241.061 241.293 1 35.83 ? C16 CDL 703 l 1 
HETATM 20 C C17 CDL . . . RB 51 321.421 240.445 241.493 1 36.75 ? C17 CDL 703 l 1 
HETATM 21 C C18 CDL . . . RB 51 320.637 240.277 240.177 1 36.15 ? C18 CDL 703 l 1 
HETATM 22 C CA6 CDL . . . RB 51 323.884 244.794 249.16 1 39.62 ? CA6 CDL 703 l 1 
HETATM 23 O OA8 CDL . . . RB 51 323.125 244.531 247.959 1 42.73 ? OA8 CDL 703 l 1 
HETATM 24 C CA7 CDL . . . RB 51 322.025 243.622 248.157 1 43.97 ? CA7 CDL 703 l 1 
HETATM 25 O OA9 CDL . . . RB 51 321.357 243.707 249.157 1 46.85 ? OA9 CDL 703 l 1 
HETATM 26 C C31 CDL . . . RB 51 321.701 242.541 247.138 1 44.16 ? C31 CDL 703 l 1 
HETATM 27 C C32 CDL . . . RB 51 320.681 242.981 246.133 1 43.38 ? C32 CDL 703 l 1 
HETATM 28 C C33 CDL . . . RB 51 321.31 243.687 244.972 1 43.4 ? C33 CDL 703 l 1 
HETATM 29 C C34 CDL . . . RB 51 320.354 243.701 243.758 1 41.8 ? C34 CDL 703 l 1 
HETATM 30 C C35 CDL . . . RB 51 320.627 244.866 242.778 1 41.76 ? C35 CDL 703 l 1 
HETATM 31 C C36 CDL . . . RB 51 319.344 245.652 242.42 1 41.79 ? C36 CDL 703 l 1 
HETATM 32 C C37 CDL . . . RB 51 319.44 246.271 241.015 1 42.6 ? C37 CDL 703 l 1 
HETATM 33 C C38 CDL . . . RB 51 318.269 247.262 240.715 1 42.54 ? C38 CDL 703 l 1 
HETATM 34 C CB2 CDL . . . RB 51 321.349 246.681 252.482 1 30.23 ? CB2 CDL 703 l 1 
HETATM 35 O OB2 CDL . . . RB 51 321.587 247.246 251.206 1 27.6 ? OB2 CDL 703 l 1 
HETATM 36 P PB2 CDL . . . RB 51 321.598 248.857 251.108 1 26.02 ? PB2 CDL 703 l 1 
HETATM 37 O OB3 CDL . . . RB 51 320.285 249.395 251.567 1 33.24 ? OB3 CDL 703 l 1 
HETATM 38 O OB4 CDL . . . RB 51 322.711 249.419 251.942 1 22.74 ? OB4 CDL 703 l 1 
HETATM 39 O OB5 CDL . . . RB 51 321.814 249.264 249.596 1 31.65 ? OB5 CDL 703 l 1 
HETATM 40 C CB3 CDL . . . RB 51 321.23 250.486 249.186 1 37.21 ? CB3 CDL 703 l 1 
HETATM 41 C CB4 CDL . . . RB 51 320.279 250.179 248.046 1 40.27 ? CB4 CDL 703 l 1 
HETATM 42 O OB6 CDL . . . RB 51 320.5 248.889 247.541 1 43.7 ? OB6 CDL 703 l 1 
HETATM 43 C CB5 CDL . . . RB 51 321.591 248.694 246.638 1 45.63 ? CB5 CDL 703 l 1 
HETATM 44 O OB7 CDL . . . RB 51 322.744 248.858 246.999 1 46.77 ? OB7 CDL 703 l 1 
HETATM 45 C C51 CDL . . . RB 51 321.323 248.233 245.199 1 45.76 ? C51 CDL 703 l 1 
HETATM 46 C C52 CDL . . . RB 51 322.255 248.929 244.197 1 46.92 ? C52 CDL 703 l 1 
HETATM 47 C C53 CDL . . . RB 51 321.636 248.954 242.798 1 45.4 ? C53 CDL 703 l 1 
HETATM 48 C C54 CDL . . . RB 51 321.585 250.378 242.24 1 44.32 ? C54 CDL 703 l 1 
HETATM 49 C C55 CDL . . . RB 51 321.525 250.375 240.701 1 43.74 ? C55 CDL 703 l 1 
HETATM 50 C C56 CDL . . . RB 51 321.446 251.795 240.15 1 40.3 ? C56 CDL 703 l 1 
HETATM 51 C C57 CDL . . . RB 51 321.598 251.855 238.623 1 38.74 ? C57 CDL 703 l 1 
HETATM 52 C C58 CDL . . . RB 51 321.615 253.284 238.121 1 32.32 ? C58 CDL 703 l 1 
HETATM 53 C CB6 CDL . . . RB 51 320.41 251.252 246.961 1 41.86 ? CB6 CDL 703 l 1 
HETATM 54 O OB8 CDL . . . RB 51 319.455 250.977 245.949 1 43.37 ? OB8 CDL 703 l 1 
HETATM 55 C CB7 CDL . . . RB 51 318.111 251.465 246.207 1 42.26 ? CB7 CDL 703 l 1 
HETATM 56 O OB9 CDL . . . RB 51 317.595 251.325 247.279 1 39.32 ? OB9 CDL 703 l 1 
HETATM 57 C C71 CDL . . . RB 51 317.309 252.178 245.088 1 43.59 ? C71 CDL 703 l 1 
HETATM 58 C C72 CDL . . . RB 51 317.069 251.288 243.87 1 44.28 ? C72 CDL 703 l 1 
HETATM 59 C C73 CDL . . . RB 51 317.118 252.132 242.578 1 45.04 ? C73 CDL 703 l 1 
HETATM 60 C C74 CDL . . . RB 51 316.151 253.31 242.61 1 45.76 ? C74 CDL 703 l 1 
HETATM 61 C C75 CDL . . . RB 51 316.026 253.957 241.212 1 46.23 ? C75 CDL 703 l 1 
HETATM 62 C C76 CDL . . . RB 51 316.218 252.931 240.088 1 47.48 ? C76 CDL 703 l 1 
HETATM 63 C C77 CDL . . . RB 51 316.164 253.581 238.678 1 47.09 ? C77 CDL 703 l 1 
HETATM 64 C C78 CDL . . . RB 51 317.403 253.246 237.838 1 44.38 ? C78 CDL 703 l 1 
#
_model_server_stats.io_time_ms              27 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    102 
_model_server_stats.query_time_ms           238 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           64 
#