data_3O6X
#
_model_server_result.job_id            FiSgdyZDPvtw7TFJWLuOxg 
_model_server_result.datetime_utc      '2024-10-20 00:42:02' 
_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          3o6x 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"CA","auth_seq_id":4001}' 
#
_entry.id    3O6X 
#
_exptl.entry_id    3O6X 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    6 
_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            3O6X 
_cell.length_a            198.25 
_cell.length_b            203.96 
_cell.length_c            234.59 
_cell.Z_PDB               48 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3O6X 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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,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 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 J N N 
? 4 Q N N 
? 4 W N N 
? 4 CA N N 
? 4 IA N N 
? 4 OA 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
metalc ? metalc1 A OE2 GLU 215 A GLU 215 1_555 G MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? 
metalc ? metalc2 A OE1 GLU 215 A GLU 215 1_555 G MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.958 ? 
metalc ? metalc3 A OE2 GLU 286 A GLU 286 1_555 H MG MG . A MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? 
metalc ? metalc4 A OE2 GLU 472 A GLU 472 1_555 G MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.818 ? 
metalc ? metalc5 G MG MG . A MG 1001 1_555 I O3A P3S . A P3S 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.897 ? 
metalc ? metalc6 G MG MG . A MG 1001 1_555 J O1B ADP . A ADP 4001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? 
metalc ? metalc7 B OE2 GLU 215 B GLU 215 1_555 N MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? 
metalc ? metalc8 B OE1 GLU 215 B GLU 215 1_555 N MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.647 ? 
metalc ? metalc9 B OE1 GLU 217 B GLU 217 1_555 O MG MG . B MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.881 ? 
metalc ? metalc10 B OE1 GLU 286 B GLU 286 1_555 O MG MG . B MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.601 ? 
metalc ? metalc11 B OE2 GLU 472 B GLU 472 1_555 N MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? 
metalc ? metalc12 N MG MG . B MG 1001 1_555 Q O1B ADP . B ADP 4001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? 
metalc ? metalc13 O MG MG . B MG 2001 1_555 P O3A P3S . B P3S 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.637 ? 
metalc ? metalc14 C OE2 GLU 215 C GLU 215 1_555 T MG MG . C MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? 
metalc ? metalc15 C OE1 GLU 215 C GLU 215 1_555 T MG MG . C MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.703 ? 
metalc ? metalc16 C OE1 GLU 217 C GLU 217 1_555 U MG MG . C MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.836 ? 
metalc ? metalc17 C OE1 GLU 286 C GLU 286 1_555 U MG MG . C MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.589 ? 
metalc ? metalc18 C OE2 GLU 472 C GLU 472 1_555 T MG MG . C MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? 
metalc ? metalc19 T MG MG . C MG 1001 1_555 W O1B ADP . C ADP 4001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? 
metalc ? metalc20 U MG MG . C MG 2001 1_555 V O3A P3S . C P3S 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.616 ? 
metalc ? metalc21 D OE2 GLU 215 D GLU 215 1_555 Z MG MG . D MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? 
metalc ? metalc22 D OE1 GLU 215 D GLU 215 1_555 Z MG MG . D MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.663 ? 
metalc ? metalc23 D OE1 GLU 217 D GLU 217 1_555 AA MG MG . D MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.853 ? 
metalc ? metalc24 D OE1 GLU 286 D GLU 286 1_555 AA MG MG . D MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.585 ? 
metalc ? metalc25 D OE2 GLU 472 D GLU 472 1_555 Z MG MG . D MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? 
metalc ? metalc26 Z MG MG . D MG 1001 1_555 CA O1B ADP . D ADP 4001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? 
metalc ? metalc27 AA MG MG . D MG 2001 1_555 BA O3A P3S . D P3S 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.625 ? 
metalc ? metalc28 E OE2 GLU 215 E GLU 215 1_555 FA MG MG . E MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? 
metalc ? metalc29 E OE1 GLU 215 E GLU 215 1_555 FA MG MG . E MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? 
metalc ? metalc30 E OE1 GLU 217 E GLU 217 1_555 GA MG MG . E MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.87 ? 
metalc ? metalc31 E OE1 GLU 286 E GLU 286 1_555 GA MG MG . E MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.587 ? 
metalc ? metalc32 E OE2 GLU 472 E GLU 472 1_555 FA MG MG . E MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? 
metalc ? metalc33 FA MG MG . E MG 1001 1_555 IA O1B ADP . E ADP 4001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? 
metalc ? metalc34 GA MG MG . E MG 2001 1_555 HA O3A P3S . E P3S 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.648 ? 
metalc ? metalc35 F OE2 GLU 215 F GLU 215 1_555 LA MG MG . F MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? 
metalc ? metalc36 F OE1 GLU 215 F GLU 215 1_555 LA MG MG . F MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.635 ? 
metalc ? metalc37 F OE1 GLU 217 F GLU 217 1_555 MA MG MG . F MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.833 ? 
metalc ? metalc38 F OE1 GLU 286 F GLU 286 1_555 MA MG MG . F MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.602 ? 
metalc ? metalc39 F OE2 GLU 472 F GLU 472 1_555 LA MG MG . F MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? 
metalc ? metalc40 LA MG MG . F MG 1001 1_555 OA O1B ADP . F ADP 4001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? 
metalc ? metalc41 MA MG MG . F MG 2001 1_555 NA O3A P3S . F P3S 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.625 ? 
#
_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                     3O6X 
_atom_sites.fract_transf_matrix[1][1]    0.005044 
_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]    0.004903 
_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]    0.004263 
_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
G 2 MG A 1 1001 1001 MG MG . 
H 2 MG A 1 2001 2001 MG MG . 
I 3 P3S A 1 3001 3001 P3S P3S . 
J 4 ADP A 1 4001 4001 ADP ADP . 
K 5 CL A 1 5001 5001 CL CL . 
L 5 CL A 1 6001 6001 CL CL . 
M 5 CL A 1 730 5001 CL CL . 
N 2 MG B 1 1001 1001 MG MG . 
O 2 MG B 1 2001 2001 MG MG . 
P 3 P3S B 1 3001 3001 P3S P3S . 
Q 4 ADP B 1 4001 4001 ADP ADP . 
R 5 CL B 1 5001 5001 CL CL . 
S 5 CL B 1 6001 6001 CL CL . 
T 2 MG C 1 1001 1001 MG MG . 
U 2 MG C 1 2001 2001 MG MG . 
V 3 P3S C 1 3001 3001 P3S P3S . 
W 4 ADP C 1 4001 4001 ADP ADP . 
X 5 CL C 1 5001 5001 CL CL . 
Y 5 CL C 1 6001 6001 CL CL . 
Z 2 MG D 1 1001 1001 MG MG . 
AA 2 MG D 1 2001 2001 MG MG . 
BA 3 P3S D 1 3001 3001 P3S P3S . 
CA 4 ADP D 1 4001 4001 ADP ADP . 
DA 5 CL D 1 5001 5001 CL CL . 
EA 5 CL D 1 6001 6001 CL CL . 
FA 2 MG E 1 1001 1001 MG MG . 
GA 2 MG E 1 2001 2001 MG MG . 
HA 3 P3S E 1 3001 3001 P3S P3S . 
IA 4 ADP E 1 4001 4001 ADP ADP . 
JA 5 CL E 1 5001 5001 CL CL . 
KA 5 CL E 1 6001 6001 CL CL . 
LA 2 MG F 1 1001 1001 MG MG . 
MA 2 MG F 1 2001 2001 MG MG . 
NA 3 P3S F 1 3001 3001 P3S P3S . 
OA 4 ADP F 1 4001 4001 ADP ADP . 
PA 5 CL F 1 6001 6001 CL CL . 
#
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 . . . CA 4 60.585 87.096 194.402 1 93.09 ? PB ADP 4001 D 1 
HETATM 2 O O1B ADP . . . CA 4 59.969 86.951 195.74 1 93.46 ? O1B ADP 4001 D 1 
HETATM 3 O O2B ADP . . . CA 4 59.7 87.07 193.055 1 93.9 ? O2B ADP 4001 D 1 
HETATM 4 O O3B ADP . . . CA 4 62.016 87.807 194.195 1 97.06 ? O3B ADP 4001 D 1 
HETATM 5 P PA ADP . . . CA 4 62.049 85.164 192.94 1 97.01 ? PA ADP 4001 D 1 
HETATM 6 O O1A ADP . . . CA 4 62.802 86.296 192.354 1 93.55 ? O1A ADP 4001 D 1 
HETATM 7 O O2A ADP . . . CA 4 63.037 84.008 193.474 1 100.45 ? O2A ADP 4001 D 1 
HETATM 8 O O3A ADP . . . CA 4 61.158 85.6 194.212 1 94.68 ? O3A ADP 4001 D 1 
HETATM 9 O O5' ADP . . . CA 4 61.04 84.459 191.899 1 102.25 ? O5' ADP 4001 D 1 
HETATM 10 C C5' ADP . . . CA 4 60.261 85.246 190.99 1 105.84 ? C5' ADP 4001 D 1 
HETATM 11 C C4' ADP . . . CA 4 59.224 84.39 190.258 1 107.18 ? C4' ADP 4001 D 1 
HETATM 12 O O4' ADP . . . CA 4 58.396 85.209 189.414 1 109.18 ? O4' ADP 4001 D 1 
HETATM 13 C C3' ADP . . . CA 4 59.873 83.351 189.338 1 107.43 ? C3' ADP 4001 D 1 
HETATM 14 O O3' ADP . . . CA 4 59.264 82.075 189.553 1 105.71 ? O3' ADP 4001 D 1 
HETATM 15 C C2' ADP . . . CA 4 59.482 83.863 187.952 1 108.06 ? C2' ADP 4001 D 1 
HETATM 16 O O2' ADP . . . CA 4 59.386 82.763 187.044 1 104.79 ? O2' ADP 4001 D 1 
HETATM 17 C C1' ADP . . . CA 4 58.081 84.355 188.306 1 113.48 ? C1' ADP 4001 D 1 
HETATM 18 N N9 ADP . . . CA 4 57.489 85.109 187.179 1 116.89 ? N9 ADP 4001 D 1 
HETATM 19 C C8 ADP . . . CA 4 58.032 86.165 186.576 1 116.33 ? C8 ADP 4001 D 1 
HETATM 20 N N7 ADP . . . CA 4 57.23 86.579 185.597 1 117.46 ? N7 ADP 4001 D 1 
HETATM 21 C C5 ADP . . . CA 4 56.167 85.782 185.575 1 118.9 ? C5 ADP 4001 D 1 
HETATM 22 C C6 ADP . . . CA 4 55.018 85.725 184.796 1 117.4 ? C6 ADP 4001 D 1 
HETATM 23 N N6 ADP . . . CA 4 54.826 86.597 183.812 1 116.42 ? N6 ADP 4001 D 1 
HETATM 24 N N1 ADP . . . CA 4 54.112 84.77 185.049 1 117.2 ? N1 ADP 4001 D 1 
HETATM 25 C C2 ADP . . . CA 4 54.3 83.894 186.02 1 116.1 ? C2 ADP 4001 D 1 
HETATM 26 N N3 ADP . . . CA 4 55.382 83.918 186.779 1 117.78 ? N3 ADP 4001 D 1 
HETATM 27 C C4 ADP . . . CA 4 56.33 84.845 186.585 1 118.94 ? C4 ADP 4001 D 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    57 
_model_server_stats.query_time_ms           310 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#