data_4JAV
#
_model_server_result.job_id            riRkNq3T7xX26x06Nu-LIw 
_model_server_result.datetime_utc      '2025-01-27 04:31:26' 
_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          4jav 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":505}' 
#
_entry.id    4JAV 
#
_exptl.entry_id    4JAV 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            4JAV 
_cell.length_a            119.319 
_cell.length_b            143.928 
_cell.length_c            138.969 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4JAV 
_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    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_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
? 5 H N N 
? 5 M 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 99 A CYS 330 1_555 A SG CYS 128 A CYS 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf2 B SG CYS 99 B CYS 330 1_555 B SG CYS 128 B CYS 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
covale ? covale1 C C LEU 52 C LEU 52 1_555 C N BFD 53 C BFD 53 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? 
covale ? covale2 C C BFD 53 C BFD 53 1_555 C N ILE 54 C ILE 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale3 D C LEU 52 D LEU 52 1_555 D N BFD 53 D BFD 53 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale4 D C BFD 53 D BFD 53 1_555 D N ILE 54 D ILE 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
metalc ? metalc1 A OD1 ASN 149 A ASN 380 1_555 G MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? 
metalc ? metalc2 F O3 SO4 . A SO4 502 1_555 G MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.729 ? 
metalc ? metalc3 G MG MG . A MG 503 1_555 H O1B ADP . A ADP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.462 ? 
metalc ? metalc4 G MG MG . A MG 503 1_555 H O1A ADP . A ADP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.485 ? 
metalc ? metalc5 B OD1 ASN 149 B ASN 380 1_555 L MG MG . B MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.75 ? 
metalc ? metalc6 L MG MG . B MG 504 1_555 M O1A ADP . B ADP 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.489 ? 
metalc ? metalc7 C OD1 ASP 10 C ASP 10 1_555 O MG MG . C MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? 
metalc ? metalc8 C OD2 BFD 53 C BFD 53 1_555 O MG MG . C MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? 
metalc ? metalc9 C O MET 55 C MET 55 1_555 O MG MG . C MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? 
metalc ? metalc10 D OD1 ASP 10 D ASP 10 1_555 P MG MG . D MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? 
metalc ? metalc11 D OD2 BFD 53 D BFD 53 1_555 P MG MG . D MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? 
metalc ? metalc12 D O MET 55 D MET 55 1_555 P MG MG . D MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? 
#
_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                     4JAV 
_atom_sites.fract_transf_matrix[1][1]    0.008381 
_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]    0.006948 
_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]    0.007196 
_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 SO4 A 1 501 2 SO4 SO4 . 
F 3 SO4 A 1 502 4 SO4 SO4 . 
G 4 MG A 1 503 4 MG MG . 
H 5 ADP A 1 504 1 ADP ADP . 
I 3 SO4 B 1 501 1 SO4 SO4 . 
J 3 SO4 B 1 502 3 SO4 SO4 . 
K 3 SO4 B 1 503 5 SO4 SO4 . 
L 4 MG B 1 504 1 MG MG . 
M 5 ADP B 1 505 1 ADP ADP . 
N 6 CL B 1 506 1 CL CL . 
O 4 MG C 1 201 2 MG MG . 
P 4 MG D 1 201 3 MG MG . 
Q 7 HOH A 1 601 1 HOH HOH . 
Q 7 HOH A 2 602 3 HOH HOH . 
Q 7 HOH A 3 603 5 HOH HOH . 
Q 7 HOH A 4 604 6 HOH HOH . 
Q 7 HOH A 5 605 9 HOH HOH . 
Q 7 HOH A 6 606 10 HOH HOH . 
Q 7 HOH A 7 607 11 HOH HOH . 
Q 7 HOH A 8 608 13 HOH HOH . 
R 7 HOH B 1 601 2 HOH HOH . 
S 7 HOH C 1 301 4 HOH HOH . 
S 7 HOH C 2 302 7 HOH HOH . 
S 7 HOH C 3 303 8 HOH HOH . 
S 7 HOH C 4 304 12 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 . . . M 5 25.466 -5.037 9.323 1 70.13 ? PB ADP 505 B 1 
HETATM 2 O O1B ADP . . . M 5 26.196 -4.061 10.208 1 70.8 ? O1B ADP 505 B 1 
HETATM 3 O O2B ADP . . . M 5 25.277 -4.552 7.909 1 71.36 ? O2B ADP 505 B 1 
HETATM 4 O O3B ADP . . . M 5 25.928 -6.465 9.464 1 71.41 ? O3B ADP 505 B 1 
HETATM 5 P PA ADP . . . M 5 23.67 -5.499 11.431 1 71.61 ? PA ADP 505 B 1 
HETATM 6 O O1A ADP . . . M 5 24.973 -5.604 12.19 1 70.63 ? O1A ADP 505 B 1 
HETATM 7 O O2A ADP . . . M 5 22.711 -6.667 11.436 1 70.98 ? O2A ADP 505 B 1 
HETATM 8 O O3A ADP . . . M 5 23.969 -5.09 9.901 1 70.53 ? O3A ADP 505 B 1 
HETATM 9 O O5' ADP . . . M 5 22.876 -4.197 11.952 1 72.26 ? O5' ADP 505 B 1 
HETATM 10 C C5' ADP . . . M 5 21.679 -3.768 11.297 1 72.64 ? C5' ADP 505 B 1 
HETATM 11 C C4' ADP . . . M 5 21.742 -2.295 10.903 1 72.9 ? C4' ADP 505 B 1 
HETATM 12 O O4' ADP . . . M 5 21.499 -1.453 12.036 1 73.65 ? O4' ADP 505 B 1 
HETATM 13 C C3' ADP . . . M 5 23.092 -1.874 10.34 1 73.19 ? C3' ADP 505 B 1 
HETATM 14 O O3' ADP . . . M 5 23.132 -1.978 8.914 1 72.86 ? O3' ADP 505 B 1 
HETATM 15 C C2' ADP . . . M 5 23.257 -0.441 10.802 1 74.1 ? C2' ADP 505 B 1 
HETATM 16 O O2' ADP . . . M 5 22.851 0.481 9.788 1 74.95 ? O2' ADP 505 B 1 
HETATM 17 C C1' ADP . . . M 5 22.36 -0.308 12.02 1 74.37 ? C1' ADP 505 B 1 
HETATM 18 N N9 ADP . . . M 5 23.229 -0.276 13.225 1 74.97 ? N9 ADP 505 B 1 
HETATM 19 C C8 ADP . . . M 5 23.65 -1.346 13.928 1 74.9 ? C8 ADP 505 B 1 
HETATM 20 N N7 ADP . . . M 5 24.436 -0.974 14.969 1 75.08 ? N7 ADP 505 B 1 
HETATM 21 C C5 ADP . . . M 5 24.536 0.366 14.943 1 74.59 ? C5 ADP 505 B 1 
HETATM 22 C C6 ADP . . . M 5 25.215 1.407 15.755 1 74.12 ? C6 ADP 505 B 1 
HETATM 23 N N6 ADP . . . M 5 25.966 1.076 16.831 1 75.52 ? N6 ADP 505 B 1 
HETATM 24 N N1 ADP . . . M 5 25.061 2.699 15.387 1 74.62 ? N1 ADP 505 B 1 
HETATM 25 C C2 ADP . . . M 5 24.317 3.048 14.318 1 75.79 ? C2 ADP 505 B 1 
HETATM 26 N N3 ADP . . . M 5 23.674 2.157 13.536 1 76.43 ? N3 ADP 505 B 1 
HETATM 27 C C4 ADP . . . M 5 23.74 0.824 13.791 1 75.49 ? C4 ADP 505 B 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    17 
_model_server_stats.query_time_ms           316 
_model_server_stats.encode_time_ms          11 
_model_server_stats.element_count           27 
#