data_5XTD
#
_model_server_result.job_id            '_IpwKP5iWX0Q9BJFjnUA_g' 
_model_server_result.datetime_utc      '2024-10-31 07:19:51' 
_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":"SB","auth_seq_id":704}' 
#
_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 . . . SB 51 291.725 271.843 221.383 1 26.43 ? C1 CDL 704 l 1 
HETATM 2 O O1 CDL . . . SB 51 292.244 271.612 222.687 1 26.57 ? O1 CDL 704 l 1 
HETATM 3 C CA2 CDL . . . SB 51 292.201 270.674 220.495 1 30.23 ? CA2 CDL 704 l 1 
HETATM 4 O OA2 CDL . . . SB 51 292.355 269.546 221.351 1 36.05 ? OA2 CDL 704 l 1 
HETATM 5 P PA1 CDL . . . SB 51 292.305 268.07 220.744 1 41.48 ? PA1 CDL 704 l 1 
HETATM 6 O OA3 CDL . . . SB 51 292.14 268.144 219.244 1 43.86 ? OA3 CDL 704 l 1 
HETATM 7 O OA4 CDL . . . SB 51 293.585 267.362 221.063 1 41.35 ? OA4 CDL 704 l 1 
HETATM 8 O OA5 CDL . . . SB 51 291.087 267.24 221.35 1 41.39 ? OA5 CDL 704 l 1 
HETATM 9 C CA3 CDL . . . SB 51 291.356 265.918 221.899 1 40.68 ? CA3 CDL 704 l 1 
HETATM 10 C CA4 CDL . . . SB 51 291.444 266.038 223.41 1 41.61 ? CA4 CDL 704 l 1 
HETATM 11 O OA6 CDL . . . SB 51 290.863 264.874 223.986 1 41.23 ? OA6 CDL 704 l 1 
HETATM 12 C CA5 CDL . . . SB 51 290.708 264.891 225.433 1 43.07 ? CA5 CDL 704 l 1 
HETATM 13 O OA7 CDL . . . SB 51 289.649 265.253 225.935 1 44.55 ? OA7 CDL 704 l 1 
HETATM 14 C C11 CDL . . . SB 51 291.87 264.424 226.353 1 43.5 ? C11 CDL 704 l 1 
HETATM 15 C C12 CDL . . . SB 51 291.381 264.25 227.791 1 46.08 ? C12 CDL 704 l 1 
HETATM 16 C C13 CDL . . . SB 51 292.292 263.338 228.627 1 47.48 ? C13 CDL 704 l 1 
HETATM 17 C C14 CDL . . . SB 51 291.916 263.389 230.124 1 48.82 ? C14 CDL 704 l 1 
HETATM 18 C C15 CDL . . . SB 51 293.12 263.22 231.011 1 50.4 ? C15 CDL 704 l 1 
HETATM 19 C C16 CDL . . . SB 51 293.136 264.217 232.207 1 51.05 ? C16 CDL 704 l 1 
HETATM 20 C C17 CDL . . . SB 51 294.511 264.252 232.871 1 50.9 ? C17 CDL 704 l 1 
HETATM 21 C C18 CDL . . . SB 51 294.421 264.404 234.398 1 49.98 ? C18 CDL 704 l 1 
HETATM 22 C CA6 CDL . . . SB 51 290.712 267.302 223.88 1 42.59 ? CA6 CDL 704 l 1 
HETATM 23 O OA8 CDL . . . SB 51 291.652 268.41 223.92 1 45.3 ? OA8 CDL 704 l 1 
HETATM 24 C CA7 CDL . . . SB 51 291.246 269.557 224.709 1 44.46 ? CA7 CDL 704 l 1 
HETATM 25 O OA9 CDL . . . SB 51 290.98 270.603 224.169 1 46.67 ? OA9 CDL 704 l 1 
HETATM 26 C C31 CDL . . . SB 51 291.151 269.456 226.227 1 43.53 ? C31 CDL 704 l 1 
HETATM 27 C C32 CDL . . . SB 51 292.447 269.772 226.914 1 42.85 ? C32 CDL 704 l 1 
HETATM 28 C C33 CDL . . . SB 51 293.118 268.556 227.48 1 43.71 ? C33 CDL 704 l 1 
HETATM 29 C C34 CDL . . . SB 51 293.096 268.555 229.022 1 45.58 ? C34 CDL 704 l 1 
HETATM 30 C C35 CDL . . . SB 51 294.522 268.506 229.607 1 46.68 ? C35 CDL 704 l 1 
HETATM 31 C C36 CDL . . . SB 51 294.531 268.295 231.14 1 47.42 ? C36 CDL 704 l 1 
HETATM 32 C C37 CDL . . . SB 51 293.888 269.453 231.924 1 47.04 ? C37 CDL 704 l 1 
HETATM 33 C C38 CDL . . . SB 51 294.536 269.597 233.339 1 47.39 ? C38 CDL 704 l 1 
HETATM 34 C CB2 CDL . . . SB 51 292.192 273.229 220.93 1 22.53 ? CB2 CDL 704 l 1 
HETATM 35 O OB2 CDL . . . SB 51 291.852 274.177 221.941 1 15.55 ? OB2 CDL 704 l 1 
HETATM 36 P PB2 CDL . . . SB 51 290.746 275.319 221.606 1 11.56 ? PB2 CDL 704 l 1 
HETATM 37 O OB3 CDL . . . SB 51 291.348 276.357 220.718 1 11.22 ? OB3 CDL 704 l 1 
HETATM 38 O OB4 CDL . . . SB 51 289.581 274.692 220.892 1 13.22 ? OB4 CDL 704 l 1 
HETATM 39 O OB5 CDL . . . SB 51 290.232 276.003 222.955 1 16.06 ? OB5 CDL 704 l 1 
HETATM 40 C CB3 CDL . . . SB 51 291.176 276.545 223.876 1 26.24 ? CB3 CDL 704 l 1 
HETATM 41 C CB4 CDL . . . SB 51 290.732 277.947 224.287 1 32.14 ? CB4 CDL 704 l 1 
HETATM 42 O OB6 CDL . . . SB 51 291.43 278.887 223.515 1 35.51 ? OB6 CDL 704 l 1 
HETATM 43 C CB5 CDL . . . SB 51 290.81 280.169 223.364 1 37.72 ? CB5 CDL 704 l 1 
HETATM 44 O OB7 CDL . . . SB 51 289.645 280.252 223.004 1 39.71 ? OB7 CDL 704 l 1 
HETATM 45 C C51 CDL . . . SB 51 291.618 281.454 223.645 1 38.15 ? C51 CDL 704 l 1 
HETATM 46 C C52 CDL . . . SB 51 291.156 282.224 224.904 1 37.84 ? C52 CDL 704 l 1 
HETATM 47 C C53 CDL . . . SB 51 292.322 282.756 225.751 1 35.62 ? C53 CDL 704 l 1 
HETATM 48 C C54 CDL . . . SB 51 292.484 281.969 227.067 1 35.36 ? C54 CDL 704 l 1 
HETATM 49 C C55 CDL . . . SB 51 293.363 282.701 228.111 1 33.36 ? C55 CDL 704 l 1 
HETATM 50 C C56 CDL . . . SB 51 293.462 281.924 229.425 1 32.5 ? C56 CDL 704 l 1 
HETATM 51 C C57 CDL . . . SB 51 294.386 282.593 230.452 1 32.16 ? C57 CDL 704 l 1 
HETATM 52 C C58 CDL . . . SB 51 294.402 281.833 231.765 1 31.26 ? C58 CDL 704 l 1 
HETATM 53 C CB6 CDL . . . SB 51 291.033 278.179 225.777 1 35.7 ? CB6 CDL 704 l 1 
HETATM 54 O OB8 CDL . . . SB 51 290.214 277.328 226.577 1 41.59 ? OB8 CDL 704 l 1 
HETATM 55 C CB7 CDL . . . SB 51 290.671 277.141 227.947 1 44.06 ? CB7 CDL 704 l 1 
HETATM 56 O OB9 CDL . . . SB 51 290.147 277.748 228.845 1 46.92 ? OB9 CDL 704 l 1 
HETATM 57 C C71 CDL . . . SB 51 291.832 276.148 228.26 1 45.64 ? C71 CDL 704 l 1 
HETATM 58 C C72 CDL . . . SB 51 292.297 276.214 229.722 1 45.76 ? C72 CDL 704 l 1 
HETATM 59 C C73 CDL . . . SB 51 292.722 274.829 230.276 1 44.26 ? C73 CDL 704 l 1 
HETATM 60 C C74 CDL . . . SB 51 293.228 274.896 231.715 1 45.79 ? C74 CDL 704 l 1 
HETATM 61 C C75 CDL . . . SB 51 293.981 273.603 232.129 1 44.04 ? C75 CDL 704 l 1 
HETATM 62 C C76 CDL . . . SB 51 295.158 273.885 233.085 1 43.09 ? C76 CDL 704 l 1 
HETATM 63 C C77 CDL . . . SB 51 296.263 272.777 233.051 1 42.24 ? C77 CDL 704 l 1 
HETATM 64 C C78 CDL . . . SB 51 297.512 273.107 233.885 1 40.34 ? C78 CDL 704 l 1 
#
_model_server_stats.io_time_ms              33 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    111 
_model_server_stats.query_time_ms           259 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           64 
#