data_6MSG
#
_model_server_result.job_id            LStG3g4knv17iaGa6CCUrg 
_model_server_result.datetime_utc      '2025-02-05 17:03:07' 
_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          6msg 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"XA","auth_seq_id":501}' 
#
_entry.id    6MSG 
#
_exptl.entry_id    6MSG 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          36 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    48-meric 
_pdbx_struct_assembly.oligomeric_count      48 
_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 
_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
? 36 XA N N 
? 36 EB 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 A SG CYS 633 U CYS 633 1_555 A SG CYS 659 U CYS 659 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf2 M SG CYS 236 A CYS 236 1_555 M SG CYS 270 A CYS 270 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf3 AA SG CYS 41 M CYS 41 1_555 AA SG CYS 186 M CYS 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
disulf ? disulf4 GA SG CYS 70 S CYS 43 1_555 GA SG CYS 223 S CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf5 OA SG CYS 41 m CYS 41 1_555 OA SG CYS 186 m CYS 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
disulf ? disulf6 UA SG CYS 70 s CYS 43 1_555 UA SG CYS 223 s CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
metalc ? metalc1 I NE2 HIS 112 c HIS 113 1_555 WA ZN ZN . c ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? 
metalc ? metalc2 I NE2 HIS 114 c HIS 115 1_555 WA ZN ZN . c ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? 
metalc ? metalc3 I OD2 ASP 125 c ASP 126 1_555 WA ZN ZN . c ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? 
metalc ? metalc4 YA O1B ATP . C ATP 501 1_555 ZA MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? 
metalc ? metalc5 YA O2B ATP . C ATP 501 1_555 ZA MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? 
metalc ? metalc6 AB O3G ATP . D ATP 501 1_555 BB MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? 
metalc ? metalc7 AB O1B ATP . D ATP 501 1_555 BB MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? 
metalc ? metalc8 AB O3B ATP . D ATP 501 1_555 BB MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? 
metalc ? metalc9 Q OG1 THR 195 E THR 181 1_555 DB MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? 
metalc ? metalc10 CB O2G ATP . E ATP 401 1_555 DB MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? 
metalc ? metalc11 CB O1B ATP . E ATP 401 1_555 DB MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? 
#
_chem_comp.formula           'C10 H15 N5 O10 P2' 
_chem_comp.formula_weight    427.201 
_chem_comp.id                ADP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "ADENOSINE-5'-DIPHOSPHATE" 
_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
PB O1B ADP doub 1 n n 
PB O2B ADP sing 2 n n 
PB O3B ADP sing 3 n n 
PB O3A ADP sing 4 n n 
O2B HOB2 ADP sing 5 n n 
O3B HOB3 ADP sing 6 n n 
PA O1A ADP doub 7 n n 
PA O2A ADP sing 8 n n 
PA O3A ADP sing 9 n n 
PA O5' ADP sing 10 n n 
O2A HOA2 ADP sing 11 n n 
O5' C5' ADP sing 12 n n 
C5' C4' ADP sing 13 n n 
C5' "H5'1" ADP sing 14 n n 
C5' "H5'2" ADP sing 15 n n 
C4' O4' ADP sing 16 n n 
C4' C3' ADP sing 17 n n 
C4' H4' ADP sing 18 n n 
O4' C1' ADP sing 19 n n 
C3' O3' ADP sing 20 n n 
C3' C2' ADP sing 21 n n 
C3' H3' ADP sing 22 n n 
O3' HO3' ADP sing 23 n n 
C2' O2' ADP sing 24 n n 
C2' C1' ADP sing 25 n n 
C2' H2' ADP sing 26 n n 
O2' HO2' ADP sing 27 n n 
C1' N9 ADP sing 28 n n 
C1' H1' ADP sing 29 n n 
N9 C8 ADP sing 30 n y 
N9 C4 ADP sing 31 n y 
C8 N7 ADP doub 32 n y 
C8 H8 ADP sing 33 n n 
N7 C5 ADP sing 34 n y 
C5 C6 ADP sing 35 n y 
C5 C4 ADP doub 36 n y 
C6 N6 ADP sing 37 n n 
C6 N1 ADP doub 38 n y 
N6 HN61 ADP sing 39 n n 
N6 HN62 ADP sing 40 n n 
N1 C2 ADP sing 41 n y 
C2 N3 ADP doub 42 n y 
C2 H2 ADP sing 43 n n 
N3 C4 ADP sing 44 n y 
#
_atom_sites.entry_id                     6MSG 
_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
WA 35 ZN c 1 401 401 ZN ZN . 
XA 36 ADP A 1 501 434 ADP ADP . 
YA 37 ATP C 1 501 407 ATP ATP . 
ZA 38 MG C 1 502 408 MG MG . 
AB 37 ATP D 1 501 440 ATP ATP . 
BB 38 MG D 1 502 441 MG MG . 
CB 37 ATP E 1 401 390 ATP ATP . 
DB 38 MG E 1 402 391 MG MG . 
EB 36 ADP F 1 501 440 ADP ADP . 
#
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 PB ADP . . . XA 36 239.345 250.016 182.456 1 155.12 ? PB ADP 501 A 1 
HETATM 2 O O1B ADP . . . XA 36 239.498 248.517 182.396 1 155.12 ? O1B ADP 501 A 1 
HETATM 3 O O2B ADP . . . XA 36 238.351 250.491 183.484 1 155.12 ? O2B ADP 501 A 1 
HETATM 4 O O3B ADP . . . XA 36 240.645 250.781 182.42 1 155.12 ? O3B ADP 501 A 1 
HETATM 5 P PA ADP . . . XA 36 239.412 250.284 179.666 1 155.12 ? PA ADP 501 A 1 
HETATM 6 O O1A ADP . . . XA 36 239.946 248.882 179.512 1 155.12 ? O1A ADP 501 A 1 
HETATM 7 O O2A ADP . . . XA 36 240.351 251.448 179.571 1 155.12 ? O2A ADP 501 A 1 
HETATM 8 O O3A ADP . . . XA 36 238.636 250.399 181.068 1 155.12 ? O3A ADP 501 A 1 
HETATM 9 O O5' ADP . . . XA 36 238.236 250.51 178.595 1 155.12 ? O5' ADP 501 A 1 
HETATM 10 C C5' ADP . . . XA 36 237.209 251.466 178.84 1 155.12 ? C5' ADP 501 A 1 
HETATM 11 C C4' ADP . . . XA 36 236.303 251.518 177.617 1 155.12 ? C4' ADP 501 A 1 
HETATM 12 O O4' ADP . . . XA 36 235.076 252.181 177.924 1 155.12 ? O4' ADP 501 A 1 
HETATM 13 C C3' ADP . . . XA 36 236.959 252.284 176.482 1 155.12 ? C3' ADP 501 A 1 
HETATM 14 O O3' ADP . . . XA 36 237.402 251.383 175.467 1 155.12 ? O3' ADP 501 A 1 
HETATM 15 C C2' ADP . . . XA 36 235.883 253.193 175.932 1 155.12 ? C2' ADP 501 A 1 
HETATM 16 O O2' ADP . . . XA 36 235.545 252.788 174.604 1 155.12 ? O2' ADP 501 A 1 
HETATM 17 C C1' ADP . . . XA 36 234.675 253.02 176.839 1 155.12 ? C1' ADP 501 A 1 
HETATM 18 N N9 ADP . . . XA 36 234.194 254.317 177.386 1 155.12 ? N9 ADP 501 A 1 
HETATM 19 C C8 ADP . . . XA 36 234.118 254.624 178.695 1 155.12 ? C8 ADP 501 A 1 
HETATM 20 N N7 ADP . . . XA 36 233.627 255.875 178.883 1 155.12 ? N7 ADP 501 A 1 
HETATM 21 C C5 ADP . . . XA 36 233.372 256.389 177.668 1 155.12 ? C5 ADP 501 A 1 
HETATM 22 C C6 ADP . . . XA 36 232.841 257.667 177.143 1 155.12 ? C6 ADP 501 A 1 
HETATM 23 N N6 ADP . . . XA 36 232.475 258.668 177.979 1 155.12 ? N6 ADP 501 A 1 
HETATM 24 N N1 ADP . . . XA 36 232.727 257.796 175.803 1 155.12 ? N1 ADP 501 A 1 
HETATM 25 C C2 ADP . . . XA 36 233.094 256.814 174.96 1 155.12 ? C2 ADP 501 A 1 
HETATM 26 N N3 ADP . . . XA 36 233.578 255.63 175.367 1 155.12 ? N3 ADP 501 A 1 
HETATM 27 C C4 ADP . . . XA 36 233.739 255.358 176.684 1 155.12 ? C4 ADP 501 A 1 
#
_model_server_stats.io_time_ms              49 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    179 
_model_server_stats.query_time_ms           361 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           27 
#