data_5KNC
#
_model_server_result.job_id            JPBsxySsBb-SslUUxqWDPQ 
_model_server_result.datetime_utc      '2025-03-21 09:17:47' 
_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          5knc 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Z","auth_seq_id":602}' 
#
_entry.id    5KNC 
#
_exptl.entry_id    5KNC 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          7 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    3 
_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            5KNC 
_cell.length_a            121.68 
_cell.length_b            126.49 
_cell.length_c            225.26 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5KNC 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    octameric 
_pdbx_struct_assembly.oligomeric_count      8 
_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 
_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
? 7 K N N 
? 7 S N N 
? 7 Z 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 OG1 THR 246 A THR 239 1_555 I MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? 
metalc ? metalc2 I MG MG . A MG 701 1_555 J O4 SO4 . A SO4 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? 
metalc ? metalc3 I MG MG . A MG 701 1_555 K O1B ADP . A ADP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.606 ? 
metalc ? metalc4 I MG MG . A MG 701 1_555 K O3B ADP . A ADP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.414 ? 
metalc ? metalc5 I MG MG . A MG 701 1_555 DA O HOH . A HOH 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? 
metalc ? metalc6 I MG MG . A MG 701 1_555 DA O HOH . A HOH 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? 
metalc ? metalc7 B OG1 THR 246 B THR 239 1_555 R MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.941 ? 
metalc ? metalc8 R MG MG . B MG 601 1_555 S O3B ADP . B ADP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.856 ? 
metalc ? metalc9 R MG MG . B MG 601 1_555 S O2B ADP . B ADP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.739 ? 
metalc ? metalc10 R MG MG . B MG 601 1_555 EA O HOH . B HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
metalc ? metalc11 R MG MG . B MG 601 1_555 EA O HOH . B HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? 
metalc ? metalc12 R MG MG . B MG 601 1_555 EA O HOH . B HOH 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.813 ? 
metalc ? metalc13 R MG MG . B MG 601 1_555 EA O HOH . B HOH 708 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? 
metalc ? metalc14 C OG1 THR 246 C THR 239 1_555 Y MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? 
metalc ? metalc15 Y MG MG . C MG 601 1_555 Z O1B ADP . C ADP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? 
metalc ? metalc16 Y MG MG . C MG 601 1_555 FA O HOH . C HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? 
metalc ? metalc17 Y MG MG . C MG 601 1_555 FA O HOH . C HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
metalc ? metalc18 Y MG MG . C MG 601 1_555 FA O HOH . C HOH 709 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? 
#
_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                     5KNC 
_atom_sites.fract_transf_matrix[1][1]    0.008218 
_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]    0.007906 
_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]    0.004439 
_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
I 5 MG A 1 701 701 MG MG . 
J 6 SO4 A 1 702 702 SO4 SO4 . 
K 7 ADP A 1 703 703 ADP ADP . 
L 8 GOL A 1 704 704 GOL GOL . 
M 8 GOL A 1 705 705 GOL GOL . 
N 8 GOL A 1 706 706 GOL GOL . 
O 8 GOL A 1 707 707 GOL GOL . 
P 8 GOL A 1 708 708 GOL GOL . 
Q 8 GOL A 1 709 709 GOL GOL . 
R 5 MG B 1 601 601 MG MG . 
S 7 ADP B 1 602 602 ADP ADP . 
T 8 GOL B 1 603 603 GOL GOL . 
U 8 GOL B 1 604 604 GOL GOL . 
V 8 GOL B 1 605 605 GOL GOL . 
W 8 GOL B 1 606 606 GOL GOL . 
X 8 GOL B 1 607 607 GOL GOL . 
Y 5 MG C 1 601 601 MG MG . 
Z 7 ADP C 1 602 602 ADP ADP . 
AA 8 GOL D 1 501 501 GOL GOL . 
BA 8 GOL D 1 502 502 GOL GOL . 
CA 8 GOL F 1 501 501 GOL GOL . 
DA 9 HOH A 1 801 801 HOH HOH . 
DA 9 HOH A 2 802 802 HOH HOH . 
DA 9 HOH A 3 803 803 HOH HOH . 
DA 9 HOH A 4 804 804 HOH HOH . 
DA 9 HOH A 5 805 805 HOH HOH . 
DA 9 HOH A 6 806 806 HOH HOH . 
DA 9 HOH A 7 807 807 HOH HOH . 
DA 9 HOH A 8 808 808 HOH HOH . 
DA 9 HOH A 9 809 809 HOH HOH . 
DA 9 HOH A 10 810 810 HOH HOH . 
DA 9 HOH A 11 811 811 HOH HOH . 
DA 9 HOH A 12 812 812 HOH HOH . 
EA 9 HOH B 1 701 701 HOH HOH . 
EA 9 HOH B 2 702 702 HOH HOH . 
EA 9 HOH B 3 703 703 HOH HOH . 
EA 9 HOH B 4 704 704 HOH HOH . 
EA 9 HOH B 5 705 705 HOH HOH . 
EA 9 HOH B 6 706 706 HOH HOH . 
EA 9 HOH B 7 707 707 HOH HOH . 
EA 9 HOH B 8 708 708 HOH HOH . 
EA 9 HOH B 9 709 709 HOH HOH . 
EA 9 HOH B 10 710 710 HOH HOH . 
EA 9 HOH B 11 711 711 HOH HOH . 
EA 9 HOH B 12 712 712 HOH HOH . 
EA 9 HOH B 13 713 713 HOH HOH . 
EA 9 HOH B 14 714 714 HOH HOH . 
EA 9 HOH B 15 715 715 HOH HOH . 
EA 9 HOH B 16 716 716 HOH HOH . 
EA 9 HOH B 17 717 717 HOH HOH . 
EA 9 HOH B 18 718 718 HOH HOH . 
EA 9 HOH B 19 719 719 HOH HOH . 
FA 9 HOH C 1 701 701 HOH HOH . 
FA 9 HOH C 2 702 702 HOH HOH . 
FA 9 HOH C 3 703 703 HOH HOH . 
FA 9 HOH C 4 704 704 HOH HOH . 
FA 9 HOH C 5 705 705 HOH HOH . 
FA 9 HOH C 6 706 706 HOH HOH . 
FA 9 HOH C 7 707 707 HOH HOH . 
FA 9 HOH C 8 708 708 HOH HOH . 
FA 9 HOH C 9 709 709 HOH HOH . 
FA 9 HOH C 10 710 710 HOH HOH . 
FA 9 HOH C 11 711 711 HOH HOH . 
FA 9 HOH C 12 712 712 HOH HOH . 
FA 9 HOH C 13 713 713 HOH HOH . 
FA 9 HOH C 14 714 714 HOH HOH . 
FA 9 HOH C 15 715 715 HOH HOH . 
GA 9 HOH D 1 601 601 HOH HOH . 
GA 9 HOH D 2 602 602 HOH HOH . 
GA 9 HOH D 3 603 603 HOH HOH . 
GA 9 HOH D 4 604 604 HOH HOH . 
GA 9 HOH D 5 605 605 HOH HOH . 
GA 9 HOH D 6 606 606 HOH HOH . 
HA 9 HOH E 1 501 501 HOH HOH . 
HA 9 HOH E 2 502 502 HOH HOH . 
HA 9 HOH E 3 503 503 HOH HOH . 
HA 9 HOH E 4 504 504 HOH HOH . 
HA 9 HOH E 5 505 505 HOH HOH . 
HA 9 HOH E 6 506 506 HOH HOH . 
HA 9 HOH E 7 507 507 HOH HOH . 
HA 9 HOH E 8 508 508 HOH HOH . 
IA 9 HOH F 1 601 601 HOH HOH . 
IA 9 HOH F 2 602 602 HOH HOH . 
IA 9 HOH F 3 603 603 HOH HOH . 
IA 9 HOH F 4 604 604 HOH HOH . 
IA 9 HOH F 5 605 605 HOH HOH . 
IA 9 HOH F 6 606 606 HOH HOH . 
IA 9 HOH F 7 607 607 HOH HOH . 
JA 9 HOH G 1 301 301 HOH HOH . 
JA 9 HOH G 2 302 302 HOH HOH . 
JA 9 HOH G 3 303 303 HOH HOH . 
JA 9 HOH G 4 304 304 HOH HOH . 
KA 9 HOH H 1 201 201 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 . . . Z 7 12.753 8.863 -48.414 1 37.88 ? PB ADP 602 C 1 
HETATM 2 O O1B ADP . . . Z 7 11.29 8.685 -48.74 1 37.32 ? O1B ADP 602 C 1 
HETATM 3 O O2B ADP . . . Z 7 13.535 7.573 -48.421 1 36.55 ? O2B ADP 602 C 1 
HETATM 4 O O3B ADP . . . Z 7 13.019 9.76 -47.229 1 36.16 ? O3B ADP 602 C 1 
HETATM 5 P PA ADP . . . Z 7 12.372 10.154 -50.863 1 61.88 ? PA ADP 602 C 1 
HETATM 6 O O1A ADP . . . Z 7 11.692 8.931 -51.433 1 61.52 ? O1A ADP 602 C 1 
HETATM 7 O O2A ADP . . . Z 7 11.548 11.312 -50.351 1 62.51 ? O2A ADP 602 C 1 
HETATM 8 O O3A ADP . . . Z 7 13.346 9.675 -49.673 1 50.66 ? O3A ADP 602 C 1 
HETATM 9 O O5' ADP . . . Z 7 13.391 10.741 -51.958 1 53.59 ? O5' ADP 602 C 1 
HETATM 10 C C5' ADP . . . Z 7 14.775 10.91 -51.66 1 53.95 ? C5' ADP 602 C 1 
HETATM 11 C C4' ADP . . . Z 7 15.412 11.714 -52.786 1 54.51 ? C4' ADP 602 C 1 
HETATM 12 O O4' ADP . . . Z 7 16.275 10.881 -53.561 1 54.66 ? O4' ADP 602 C 1 
HETATM 13 C C3' ADP . . . Z 7 14.358 12.278 -53.727 1 54.74 ? C3' ADP 602 C 1 
HETATM 14 O O3' ADP . . . Z 7 14.208 13.686 -53.546 1 55.1 ? O3' ADP 602 C 1 
HETATM 15 C C2' ADP . . . Z 7 14.86 11.989 -55.124 1 54.67 ? C2' ADP 602 C 1 
HETATM 16 O O2' ADP . . . Z 7 15.356 13.191 -55.721 1 54.79 ? O2' ADP 602 C 1 
HETATM 17 C C1' ADP . . . Z 7 15.993 10.993 -54.956 1 54.68 ? C1' ADP 602 C 1 
HETATM 18 N N9 ADP . . . Z 7 15.514 9.675 -55.431 1 55.02 ? N9 ADP 602 C 1 
HETATM 19 C C8 ADP . . . Z 7 15.072 8.679 -54.641 1 55.46 ? C8 ADP 602 C 1 
HETATM 20 N N7 ADP . . . Z 7 14.701 7.598 -55.374 1 55.65 ? N7 ADP 602 C 1 
HETATM 21 C C5 ADP . . . Z 7 14.905 7.905 -56.667 1 55.63 ? C5 ADP 602 C 1 
HETATM 22 C C6 ADP . . . Z 7 14.724 7.219 -57.966 1 55.86 ? C6 ADP 602 C 1 
HETATM 23 N N6 ADP . . . Z 7 14.239 5.956 -58.029 1 55.71 ? N6 ADP 602 C 1 
HETATM 24 N N1 ADP . . . Z 7 15.062 7.897 -59.085 1 55.89 ? N1 ADP 602 C 1 
HETATM 25 C C2 ADP . . . Z 7 15.547 9.151 -59.037 1 55.46 ? C2 ADP 602 C 1 
HETATM 26 N N3 ADP . . . Z 7 15.737 9.833 -57.895 1 55.22 ? N3 ADP 602 C 1 
HETATM 27 C C4 ADP . . . Z 7 15.441 9.274 -56.7 1 55.17 ? C4 ADP 602 C 1 
#
_model_server_stats.io_time_ms              56 
_model_server_stats.parse_time_ms           26 
_model_server_stats.create_model_time_ms    29 
_model_server_stats.query_time_ms           276 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#