data_5CE3
#
_model_server_result.job_id            LRcJCqK46adyhQbHSEIp8Q 
_model_server_result.datetime_utc      '2024-11-01 15:39:02' 
_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          5ce3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":801}' 
#
_entry.id    5CE3 
#
_exptl.entry_id    5CE3 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          5 
_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                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          104.88 
_cell.angle_gamma         90 
_cell.entry_id            5CE3 
_cell.length_a            108.73 
_cell.length_b            121.75 
_cell.length_c            118.58 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5CE3 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,E,F,G,H,M,N 1 1 
C,D,I,J,K,L,O,P 2 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
? 5 G N N 
? 5 K 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 E O3G ATP . A ATP 401 1_555 F CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? 
metalc ? metalc2 E O1B ATP . A ATP 401 1_555 F CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? 
metalc ? metalc3 F CA CA . A CA 402 1_555 M O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? 
metalc ? metalc4 F CA CA . A CA 402 1_555 M O HOH . A HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.555 ? 
metalc ? metalc5 F CA CA . A CA 402 1_555 M O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.652 ? 
metalc ? metalc6 B OD1 ASN 186 B ASN 272 1_555 H MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? 
metalc ? metalc7 B OD2 ASP 200 B ASP 286 1_555 H MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? 
metalc ? metalc8 G O2B ADP . B ADP 801 1_555 H MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? 
metalc ? metalc9 G O2A ADP . B ADP 801 1_555 H MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? 
metalc ? metalc10 H MG MG . B MG 802 1_555 N O HOH . B HOH 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? 
metalc ? metalc11 H MG MG . B MG 802 1_555 N O HOH . B HOH 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? 
metalc ? metalc12 I O3G ATP . C ATP 401 1_555 J CA CA . C CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? 
metalc ? metalc13 I O1B ATP . C ATP 401 1_555 J CA CA . C CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.706 ? 
metalc ? metalc14 J CA CA . C CA 402 1_555 O O HOH . C HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? 
metalc ? metalc15 D OD1 ASN 186 D ASN 272 1_555 L MG MG . D MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? 
metalc ? metalc16 D OD2 ASP 200 D ASP 286 1_555 L MG MG . D MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? 
metalc ? metalc17 K O2B ADP . D ADP 801 1_555 L MG MG . D MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.93 ? 
metalc ? metalc18 K O2A ADP . D ADP 801 1_555 L MG MG . D MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? 
#
_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                     5CE3 
_atom_sites.fract_transf_matrix[1][1]    0.009197 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002444 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008214 
_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]    0.008726 
_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 ATP A 1 401 1380 ATP ATP . 
F 4 CA A 1 402 1401 CA CA . 
G 5 ADP B 1 801 730 ADP ADP . 
H 6 MG B 1 802 731 MG MG . 
I 3 ATP C 1 401 1380 ATP ATP . 
J 4 CA C 1 402 1401 CA CA . 
K 5 ADP D 1 801 730 ADP ADP . 
L 6 MG D 1 802 731 MG MG . 
M 7 HOH A 1 501 8 HOH HOH . 
M 7 HOH A 2 502 11 HOH HOH . 
M 7 HOH A 3 503 9 HOH HOH . 
N 7 HOH B 1 901 3 HOH HOH . 
N 7 HOH B 2 902 1 HOH HOH . 
N 7 HOH B 3 903 2 HOH HOH . 
O 7 HOH C 1 501 13 HOH HOH . 
P 7 HOH D 1 901 6 HOH HOH . 
P 7 HOH D 2 902 5 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 P PB ADP . . . G 5 19.965 -1.034 9.201 1 66.3 ? PB ADP 801 B 1 
HETATM 2 O O1B ADP . . . G 5 18.453 -1.076 9.208 1 67.19 ? O1B ADP 801 B 1 
HETATM 3 O O2B ADP . . . G 5 20.615 -2.394 9.269 1 68.08 ? O2B ADP 801 B 1 
HETATM 4 O O3B ADP . . . G 5 20.547 -0.029 10.175 1 61.73 ? O3B ADP 801 B 1 
HETATM 5 P PA ADP . . . G 5 21.513 -0.762 6.764 1 61.85 ? PA ADP 801 B 1 
HETATM 6 O O1A ADP . . . G 5 22.087 0.585 6.386 1 59.76 ? O1A ADP 801 B 1 
HETATM 7 O O2A ADP . . . G 5 22.423 -1.818 7.338 1 59.22 ? O2A ADP 801 B 1 
HETATM 8 O O3A ADP . . . G 5 20.24 -0.475 7.711 1 62.33 ? O3A ADP 801 B 1 
HETATM 9 O O5' ADP . . . G 5 20.812 -1.4 5.457 1 59.44 ? O5' ADP 801 B 1 
HETATM 10 C C5' ADP . . . G 5 20.326 -2.744 5.445 1 59.23 ? C5' ADP 801 B 1 
HETATM 11 C C4' ADP . . . G 5 20.84 -3.522 4.231 1 58.02 ? C4' ADP 801 B 1 
HETATM 12 O O4' ADP . . . G 5 20.703 -2.738 3.047 1 57.21 ? O4' ADP 801 B 1 
HETATM 13 C C3' ADP . . . G 5 22.308 -3.924 4.282 1 55.49 ? C3' ADP 801 B 1 
HETATM 14 O O3' ADP . . . G 5 22.515 -5.197 4.887 1 54.95 ? O3' ADP 801 B 1 
HETATM 15 C C2' ADP . . . G 5 22.732 -3.945 2.827 1 55.73 ? C2' ADP 801 B 1 
HETATM 16 O O2' ADP . . . G 5 22.542 -5.207 2.187 1 51.08 ? O2' ADP 801 B 1 
HETATM 17 C C1' ADP . . . G 5 21.8 -2.966 2.164 1 55.77 ? C1' ADP 801 B 1 
HETATM 18 N N9 ADP . . . G 5 22.503 -1.702 1.856 1 56.73 ? N9 ADP 801 B 1 
HETATM 19 C C8 ADP . . . G 5 22.531 -0.548 2.559 1 58.31 ? C8 ADP 801 B 1 
HETATM 20 N N7 ADP . . . G 5 23.28 0.388 1.917 1 57.82 ? N7 ADP 801 B 1 
HETATM 21 C C5 ADP . . . G 5 23.727 -0.178 0.781 1 56.8 ? C5 ADP 801 B 1 
HETATM 22 C C6 ADP . . . G 5 24.563 0.226 -0.372 1 56.69 ? C6 ADP 801 B 1 
HETATM 23 N N6 ADP . . . G 5 25.092 1.471 -0.452 1 55.37 ? N6 ADP 801 B 1 
HETATM 24 N N1 ADP . . . G 5 24.785 -0.699 -1.344 1 55.49 ? N1 ADP 801 B 1 
HETATM 25 C C2 ADP . . . G 5 24.274 -1.948 -1.29 1 54.7 ? C2 ADP 801 B 1 
HETATM 26 N N3 ADP . . . G 5 23.51 -2.378 -0.274 1 56.09 ? N3 ADP 801 B 1 
HETATM 27 C C4 ADP . . . G 5 23.214 -1.554 0.756 1 56.19 ? C4 ADP 801 B 1 
#
_model_server_stats.io_time_ms              35 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           310 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           27 
#