data_4F9A
#
_model_server_result.job_id            i5rkYBn-mLp6hHusRnlYLA 
_model_server_result.datetime_utc      '2024-10-19 03:52:40' 
_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          4f9a 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":601}' 
#
_entry.id    4F9A 
#
_exptl.entry_id    4F9A 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          3 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            4F9A 
_cell.length_a            61.08 
_cell.length_b            67.04 
_cell.length_c            237.05 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4F9A 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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,K,L 1 1 
C,D,H,I,J,M 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
? 3 E N N 
? 3 H 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 OD1 ASN 147 A ASN 182 1_555 F MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? 
metalc ? metalc2 A OD2 ASP 161 A ASP 196 1_555 F MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? 
metalc ? metalc3 E O2A ADP . A ADP 601 1_555 F MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.879 ? 
metalc ? metalc4 E O1B ADP . A ADP 601 1_555 F MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? 
metalc ? metalc5 F MG MG . A MG 602 1_555 K O HOH . A HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? 
metalc ? metalc6 F MG MG . A MG 602 1_555 K O HOH . A HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? 
metalc ? metalc7 B SG CYS 90 B CYS 296 1_555 G ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? 
metalc ? metalc8 B SG CYS 93 B CYS 299 1_555 G ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? 
metalc ? metalc9 B NE2 HIS 103 B HIS 309 1_555 G ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? 
metalc ? metalc10 B ND1 HIS 109 B HIS 315 1_555 G ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? 
metalc ? metalc11 C OD1 ASN 147 C ASN 182 1_555 I MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? 
metalc ? metalc12 C OD2 ASP 161 C ASP 196 1_555 I MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? 
metalc ? metalc13 H O2A ADP . C ADP 601 1_555 I MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? 
metalc ? metalc14 H O1B ADP . C ADP 601 1_555 I MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? 
metalc ? metalc15 I MG MG . C MG 602 1_555 M O HOH . C HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.939 ? 
metalc ? metalc16 I MG MG . C MG 602 1_555 M O HOH . C HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? 
metalc ? metalc17 D SG CYS 90 D CYS 296 1_555 J ZN ZN . D ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? 
metalc ? metalc18 D SG CYS 93 D CYS 299 1_555 J ZN ZN . D ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? 
metalc ? metalc19 D NE2 HIS 103 D HIS 309 1_555 J ZN ZN . D ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? 
metalc ? metalc20 D ND1 HIS 109 D HIS 315 1_555 J ZN ZN . D ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? 
#
_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                     4F9A 
_atom_sites.fract_transf_matrix[1][1]    0.016372 
_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]    0.014916 
_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]    0.004219 
_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 ADP A 1 601 1 ADP ADP . 
F 4 MG A 1 602 2 MG MG . 
G 5 ZN B 1 401 3 ZN ZN . 
H 3 ADP C 1 601 1 ADP ADP . 
I 4 MG C 1 602 2 MG MG . 
J 5 ZN D 1 401 3 ZN ZN . 
K 6 HOH A 1 701 1 HOH HOH . 
K 6 HOH A 2 702 2 HOH HOH . 
K 6 HOH A 3 703 3 HOH HOH . 
K 6 HOH A 4 704 9 HOH HOH . 
K 6 HOH A 5 705 10 HOH HOH . 
K 6 HOH A 6 706 11 HOH HOH . 
K 6 HOH A 7 707 12 HOH HOH . 
K 6 HOH A 8 708 13 HOH HOH . 
K 6 HOH A 9 709 14 HOH HOH . 
K 6 HOH A 10 710 15 HOH HOH . 
K 6 HOH A 11 711 16 HOH HOH . 
K 6 HOH A 12 712 17 HOH HOH . 
K 6 HOH A 13 713 18 HOH HOH . 
K 6 HOH A 14 714 21 HOH HOH . 
K 6 HOH A 15 715 22 HOH HOH . 
K 6 HOH A 16 716 24 HOH HOH . 
K 6 HOH A 17 717 25 HOH HOH . 
K 6 HOH A 18 718 26 HOH HOH . 
K 6 HOH A 19 719 27 HOH HOH . 
K 6 HOH A 20 720 28 HOH HOH . 
K 6 HOH A 21 721 29 HOH HOH . 
K 6 HOH A 22 722 30 HOH HOH . 
K 6 HOH A 23 723 32 HOH HOH . 
K 6 HOH A 24 724 33 HOH HOH . 
K 6 HOH A 25 725 34 HOH HOH . 
K 6 HOH A 26 726 38 HOH HOH . 
K 6 HOH A 27 727 2 HOH HOH . 
K 6 HOH A 28 728 3 HOH HOH . 
K 6 HOH A 29 729 5 HOH HOH . 
K 6 HOH A 30 730 6 HOH HOH . 
K 6 HOH A 31 731 10 HOH HOH . 
K 6 HOH A 32 732 11 HOH HOH . 
K 6 HOH A 33 733 14 HOH HOH . 
K 6 HOH A 34 734 15 HOH HOH . 
K 6 HOH A 35 735 17 HOH HOH . 
K 6 HOH A 36 736 18 HOH HOH . 
K 6 HOH A 37 737 20 HOH HOH . 
K 6 HOH A 38 738 21 HOH HOH . 
K 6 HOH A 39 739 22 HOH HOH . 
K 6 HOH A 40 740 23 HOH HOH . 
K 6 HOH A 41 741 24 HOH HOH . 
K 6 HOH A 42 742 25 HOH HOH . 
K 6 HOH A 43 743 26 HOH HOH . 
L 6 HOH B 1 501 8 HOH HOH . 
L 6 HOH B 2 502 23 HOH HOH . 
L 6 HOH B 3 503 31 HOH HOH . 
L 6 HOH B 4 504 13 HOH HOH . 
L 6 HOH B 5 505 29 HOH HOH . 
L 6 HOH B 6 506 2 HOH HOH . 
M 6 HOH C 1 701 4 HOH HOH . 
M 6 HOH C 2 702 5 HOH HOH . 
M 6 HOH C 3 703 6 HOH HOH . 
M 6 HOH C 4 704 7 HOH HOH . 
M 6 HOH C 5 705 19 HOH HOH . 
M 6 HOH C 6 706 20 HOH HOH . 
M 6 HOH C 7 707 35 HOH HOH . 
M 6 HOH C 8 708 36 HOH HOH . 
M 6 HOH C 9 709 37 HOH HOH . 
M 6 HOH C 10 710 9 HOH HOH . 
M 6 HOH C 11 711 12 HOH HOH . 
M 6 HOH C 12 712 16 HOH HOH . 
M 6 HOH C 13 713 19 HOH HOH . 
M 6 HOH C 14 714 27 HOH HOH . 
M 6 HOH C 15 715 3 HOH HOH . 
M 6 HOH C 16 716 6 HOH HOH . 
M 6 HOH C 17 717 9 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 . . . E 3 10.755 18.442 29.429 1 43.79 ? PB ADP 601 A 1 
HETATM 2 O O1B ADP . . . E 3 11.068 18.324 27.954 1 40.86 ? O1B ADP 601 A 1 
HETATM 3 O O2B ADP . . . E 3 11.976 18.059 30.249 1 50.03 ? O2B ADP 601 A 1 
HETATM 4 O O3B ADP . . . E 3 10.042 19.707 29.826 1 41.72 ? O3B ADP 601 A 1 
HETATM 5 P PA ADP . . . E 3 9.26 15.955 29.23 1 42.31 ? PA ADP 601 A 1 
HETATM 6 O O1A ADP . . . E 3 7.832 15.614 29.63 1 45.44 ? O1A ADP 601 A 1 
HETATM 7 O O2A ADP . . . E 3 9.59 15.912 27.741 1 41.3 ? O2A ADP 601 A 1 
HETATM 8 O O3A ADP . . . E 3 9.655 17.351 29.878 1 39.91 ? O3A ADP 601 A 1 
HETATM 9 O O5' ADP . . . E 3 10.186 14.867 29.979 1 38.46 ? O5' ADP 601 A 1 
HETATM 10 C C5' ADP . . . E 3 11.611 14.929 29.91 1 39.51 ? C5' ADP 601 A 1 
HETATM 11 C C4' ADP . . . E 3 12.223 13.576 29.546 1 36.23 ? C4' ADP 601 A 1 
HETATM 12 O O4' ADP . . . E 3 12.033 12.604 30.574 1 36.06 ? O4' ADP 601 A 1 
HETATM 13 C C3' ADP . . . E 3 11.648 12.943 28.298 1 38.2 ? C3' ADP 601 A 1 
HETATM 14 O O3' ADP . . . E 3 12.192 13.516 27.112 1 39.63 ? O3' ADP 601 A 1 
HETATM 15 C C2' ADP . . . E 3 11.894 11.452 28.52 1 35.37 ? C2' ADP 601 A 1 
HETATM 16 O O2' ADP . . . E 3 13.151 11.029 28.065 1 33.67 ? O2' ADP 601 A 1 
HETATM 17 C C1' ADP . . . E 3 11.861 11.286 30.037 1 35.24 ? C1' ADP 601 A 1 
HETATM 18 N N9 ADP . . . E 3 10.465 10.894 30.332 1 33.51 ? N9 ADP 601 A 1 
HETATM 19 C C8 ADP . . . E 3 9.445 11.777 30.424 1 31.9 ? C8 ADP 601 A 1 
HETATM 20 N N7 ADP . . . E 3 8.283 11.127 30.681 1 33.13 ? N7 ADP 601 A 1 
HETATM 21 C C5 ADP . . . E 3 8.562 9.82 30.754 1 29.96 ? C5 ADP 601 A 1 
HETATM 22 C C6 ADP . . . E 3 7.769 8.617 30.985 1 32.73 ? C6 ADP 601 A 1 
HETATM 23 N N6 ADP . . . E 3 6.445 8.742 31.221 1 34.35 ? N6 ADP 601 A 1 
HETATM 24 N N1 ADP . . . E 3 8.408 7.421 30.99 1 34.05 ? N1 ADP 601 A 1 
HETATM 25 C C2 ADP . . . E 3 9.737 7.363 30.771 1 34.41 ? C2 ADP 601 A 1 
HETATM 26 N N3 ADP . . . E 3 10.518 8.444 30.539 1 32.11 ? N3 ADP 601 A 1 
HETATM 27 C C4 ADP . . . E 3 9.992 9.668 30.526 1 30.06 ? C4 ADP 601 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           25 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           323 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#