data_6GR2
#
_model_server_result.job_id            GhonZF-W08vie7wqpubjag 
_model_server_result.datetime_utc      '2025-07-27 21:12:45' 
_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          6gr2 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"P","auth_seq_id":402}' 
#
_entry.id    6GR2 
#
_exptl.entry_id    6GR2 
_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    8 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         113.85 
_cell.angle_beta          102.26 
_cell.angle_gamma         101.29 
_cell.entry_id            6GR2 
_cell.length_a            78.217 
_cell.length_b            110.32 
_cell.length_c            118.234 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6GR2 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 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 
PISA dimeric 2 author_and_software_defined_assembly 3 
PISA dimeric 2 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,F,I,J,V,W,X,DA,IA 1 1 
B,K,L,M,N,EA 2 1 
C,O,P,Q,FA 2 2 
D,G,R,S,Y,Z,GA,JA 3 1 
E,H,T,U,AA,BA,CA,HA,KA 4 1 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 1_455 x-1,y,z 1 0 0 0 1 0 0 0 1 -78.217 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 J N N 
? 3 L N N 
? 3 P N N 
? 3 S N N 
? 3 U N N 
? 3 W N N 
? 3 Z N N 
? 3 BA 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 398 A CYS 391 1_555 F SG CYS 398 F CYS 391 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf2 B SG CYS 398 B CYS 391 1_555 C SG CYS 398 C CYS 391 1_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf3 D SG CYS 398 D CYS 391 1_555 G SG CYS 398 G CYS 391 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf4 E SG CYS 398 E CYS 391 1_555 H SG CYS 398 H CYS 391 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
#
_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                     6GR2 
_atom_sites.fract_transf_matrix[1][1]    0.012785 
_atom_sites.fract_transf_matrix[1][2]    0.002552 
_atom_sites.fract_transf_matrix[1][3]    0.004481 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009243 
_atom_sites.fract_transf_matrix[2][3]    0.004859 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.009778 
_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 2 GAL A 1 401 393 GAL GAL . 
J 3 ADP A 1 402 401 ADP ADP . 
K 2 GAL B 1 401 393 GAL GAL . 
L 3 ADP B 1 402 401 ADP ADP . 
M 4 SO4 B 1 403 501 SO4 SO4 . 
N 4 SO4 B 1 404 601 SO4 SO4 . 
O 2 GAL C 1 401 393 GAL GAL . 
P 3 ADP C 1 402 401 ADP ADP . 
Q 4 SO4 C 1 403 501 SO4 SO4 . 
R 2 GAL D 1 401 393 GAL GAL . 
S 3 ADP D 1 402 401 ADP ADP . 
T 2 GAL E 1 401 393 GAL GAL . 
U 3 ADP E 1 402 401 ADP ADP . 
V 2 GAL F 1 401 393 GAL GAL . 
W 3 ADP F 1 402 401 ADP ADP . 
X 4 SO4 F 1 403 501 SO4 SO4 . 
Y 2 GAL G 1 401 393 GAL GAL . 
Z 3 ADP G 1 402 401 ADP ADP . 
AA 2 GAL H 1 401 393 GAL GAL . 
BA 3 ADP H 1 402 401 ADP ADP . 
CA 4 SO4 H 1 403 501 SO4 SO4 . 
DA 5 HOH A 1 501 13 HOH HOH . 
DA 5 HOH A 2 502 30 HOH HOH . 
DA 5 HOH A 3 503 24 HOH HOH . 
DA 5 HOH A 4 504 28 HOH HOH . 
DA 5 HOH A 5 505 29 HOH HOH . 
DA 5 HOH A 6 506 20 HOH HOH . 
DA 5 HOH A 7 507 23 HOH HOH . 
DA 5 HOH A 8 508 26 HOH HOH . 
DA 5 HOH A 9 509 27 HOH HOH . 
DA 5 HOH A 10 510 115 HOH HOH . 
EA 5 HOH B 1 501 40 HOH HOH . 
EA 5 HOH B 2 502 44 HOH HOH . 
EA 5 HOH B 3 503 33 HOH HOH . 
EA 5 HOH B 4 504 35 HOH HOH . 
EA 5 HOH B 5 505 14 HOH HOH . 
EA 5 HOH B 6 506 17 HOH HOH . 
EA 5 HOH B 7 507 37 HOH HOH . 
EA 5 HOH B 8 508 41 HOH HOH . 
EA 5 HOH B 9 509 34 HOH HOH . 
EA 5 HOH B 10 510 36 HOH HOH . 
EA 5 HOH B 11 511 16 HOH HOH . 
EA 5 HOH B 12 512 18 HOH HOH . 
EA 5 HOH B 13 513 38 HOH HOH . 
EA 5 HOH B 14 514 32 HOH HOH . 
EA 5 HOH B 15 515 31 HOH HOH . 
EA 5 HOH B 16 516 42 HOH HOH . 
EA 5 HOH B 17 517 43 HOH HOH . 
FA 5 HOH C 1 501 48 HOH HOH . 
FA 5 HOH C 2 502 52 HOH HOH . 
FA 5 HOH C 3 503 110 HOH HOH . 
FA 5 HOH C 4 504 50 HOH HOH . 
FA 5 HOH C 5 505 12 HOH HOH . 
FA 5 HOH C 6 506 47 HOH HOH . 
FA 5 HOH C 7 507 49 HOH HOH . 
FA 5 HOH C 8 508 54 HOH HOH . 
FA 5 HOH C 9 509 51 HOH HOH . 
FA 5 HOH C 10 510 45 HOH HOH . 
GA 5 HOH D 1 501 55 HOH HOH . 
GA 5 HOH D 2 502 21 HOH HOH . 
GA 5 HOH D 3 503 53 HOH HOH . 
GA 5 HOH D 4 504 62 HOH HOH . 
GA 5 HOH D 5 505 59 HOH HOH . 
GA 5 HOH D 6 506 57 HOH HOH . 
GA 5 HOH D 7 507 61 HOH HOH . 
GA 5 HOH D 8 508 58 HOH HOH . 
GA 5 HOH D 9 509 2 HOH HOH . 
GA 5 HOH D 10 510 15 HOH HOH . 
GA 5 HOH D 11 511 60 HOH HOH . 
HA 5 HOH E 1 501 106 HOH HOH . 
HA 5 HOH E 2 502 71 HOH HOH . 
HA 5 HOH E 3 503 10 HOH HOH . 
HA 5 HOH E 4 504 74 HOH HOH . 
HA 5 HOH E 5 505 66 HOH HOH . 
HA 5 HOH E 6 506 67 HOH HOH . 
HA 5 HOH E 7 507 65 HOH HOH . 
HA 5 HOH E 8 508 73 HOH HOH . 
HA 5 HOH E 9 509 64 HOH HOH . 
HA 5 HOH E 10 510 69 HOH HOH . 
HA 5 HOH E 11 511 63 HOH HOH . 
HA 5 HOH E 12 512 70 HOH HOH . 
HA 5 HOH E 13 513 75 HOH HOH . 
HA 5 HOH E 14 514 72 HOH HOH . 
IA 5 HOH F 1 501 87 HOH HOH . 
IA 5 HOH F 2 502 83 HOH HOH . 
IA 5 HOH F 3 503 82 HOH HOH . 
IA 5 HOH F 4 504 19 HOH HOH . 
IA 5 HOH F 5 505 84 HOH HOH . 
IA 5 HOH F 6 506 76 HOH HOH . 
IA 5 HOH F 7 507 88 HOH HOH . 
IA 5 HOH F 8 508 85 HOH HOH . 
IA 5 HOH F 9 509 25 HOH HOH . 
IA 5 HOH F 10 510 91 HOH HOH . 
IA 5 HOH F 11 511 81 HOH HOH . 
IA 5 HOH F 12 512 68 HOH HOH . 
IA 5 HOH F 13 513 79 HOH HOH . 
IA 5 HOH F 14 514 4 HOH HOH . 
IA 5 HOH F 15 515 78 HOH HOH . 
IA 5 HOH F 16 516 92 HOH HOH . 
IA 5 HOH F 17 517 86 HOH HOH . 
IA 5 HOH F 18 518 89 HOH HOH . 
IA 5 HOH F 19 519 80 HOH HOH . 
IA 5 HOH F 20 520 77 HOH HOH . 
JA 5 HOH G 1 501 93 HOH HOH . 
JA 5 HOH G 2 502 97 HOH HOH . 
JA 5 HOH G 3 503 94 HOH HOH . 
JA 5 HOH G 4 504 6 HOH HOH . 
JA 5 HOH G 5 505 1 HOH HOH . 
JA 5 HOH G 6 506 95 HOH HOH . 
JA 5 HOH G 7 507 98 HOH HOH . 
JA 5 HOH G 8 508 99 HOH HOH . 
JA 5 HOH G 9 509 96 HOH HOH . 
KA 5 HOH H 1 501 103 HOH HOH . 
KA 5 HOH H 2 502 109 HOH HOH . 
KA 5 HOH H 3 503 113 HOH HOH . 
KA 5 HOH H 4 504 108 HOH HOH . 
KA 5 HOH H 5 505 104 HOH HOH . 
KA 5 HOH H 6 506 114 HOH HOH . 
KA 5 HOH H 7 507 8 HOH HOH . 
KA 5 HOH H 8 508 101 HOH HOH . 
KA 5 HOH H 9 509 105 HOH HOH . 
KA 5 HOH H 10 510 112 HOH HOH . 
KA 5 HOH H 11 511 9 HOH HOH . 
KA 5 HOH H 12 512 111 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 . . . P 3 -31.867 -28.795 42.261 1 45.23 ? PB ADP 402 C 1 
HETATM 2 O O1B ADP . . . P 3 -30.597 -28.77 41.447 1 41.59 ? O1B ADP 402 C 1 
HETATM 3 O O2B ADP . . . P 3 -32.557 -30.148 42.259 1 41.8 ? O2B ADP 402 C 1 
HETATM 4 O O3B ADP . . . P 3 -31.707 -28.198 43.645 1 50.36 ? O3B ADP 402 C 1 
HETATM 5 P PA ADP . . . P 3 -32.427 -26.544 40.571 1 47.13 ? PA ADP 402 C 1 
HETATM 6 O O1A ADP . . . P 3 -30.918 -26.416 40.758 1 53.08 ? O1A ADP 402 C 1 
HETATM 7 O O2A ADP . . . P 3 -33.36 -25.418 40.995 1 48.74 ? O2A ADP 402 C 1 
HETATM 8 O O3A ADP . . . P 3 -32.862 -27.797 41.469 1 46.56 ? O3A ADP 402 C 1 
HETATM 9 O O5' ADP . . . P 3 -32.86 -26.895 39.047 1 51.91 ? O5' ADP 402 C 1 
HETATM 10 C C5' ADP . . . P 3 -33.049 -28.228 38.548 1 52.36 ? C5' ADP 402 C 1 
HETATM 11 C C4' ADP . . . P 3 -33.58 -28.13 37.117 1 53.45 ? C4' ADP 402 C 1 
HETATM 12 O O4' ADP . . . P 3 -33.009 -29.075 36.174 1 53.47 ? O4' ADP 402 C 1 
HETATM 13 C C3' ADP . . . P 3 -35.095 -28.343 37.086 1 51.51 ? C3' ADP 402 C 1 
HETATM 14 O O3' ADP . . . P 3 -35.781 -27.093 36.94 1 50.11 ? O3' ADP 402 C 1 
HETATM 15 C C2' ADP . . . P 3 -35.36 -29.279 35.926 1 54.34 ? C2' ADP 402 C 1 
HETATM 16 O O2' ADP . . . P 3 -35.88 -28.519 34.84 1 58.62 ? O2' ADP 402 C 1 
HETATM 17 C C1' ADP . . . P 3 -34.016 -29.798 35.438 1 54.25 ? C1' ADP 402 C 1 
HETATM 18 N N9 ADP . . . P 3 -33.562 -31.19 35.629 1 54.71 ? N9 ADP 402 C 1 
HETATM 19 C C8 ADP . . . P 3 -32.664 -31.625 36.54 1 52.91 ? C8 ADP 402 C 1 
HETATM 20 N N7 ADP . . . P 3 -32.475 -32.973 36.438 1 52.21 ? N7 ADP 402 C 1 
HETATM 21 C C5 ADP . . . P 3 -33.257 -33.401 35.431 1 52.64 ? C5 ADP 402 C 1 
HETATM 22 C C6 ADP . . . P 3 -33.562 -34.689 34.771 1 48.62 ? C6 ADP 402 C 1 
HETATM 23 N N6 ADP . . . P 3 -32.971 -35.836 35.181 1 45.95 ? N6 ADP 402 C 1 
HETATM 24 N N1 ADP . . . P 3 -34.447 -34.674 33.747 1 50.47 ? N1 ADP 402 C 1 
HETATM 25 C C2 ADP . . . P 3 -35.049 -33.548 33.323 1 49.12 ? C2 ADP 402 C 1 
HETATM 26 N N3 ADP . . . P 3 -34.814 -32.351 33.879 1 52.43 ? N3 ADP 402 C 1 
HETATM 27 C C4 ADP . . . P 3 -33.956 -32.218 34.91 1 54.24 ? C4 ADP 402 C 1 
HETATM 28 H "H5'1" ADP . . . P 3 -33.758 -28.769 39.178 1 62.83 ? "H5'1" ADP 402 C 1 
HETATM 29 H "H5'2" ADP . . . P 3 -32.103 -28.773 38.562 1 62.83 ? "H5'2" ADP 402 C 1 
HETATM 30 H H4' ADP . . . P 3 -33.283 -27.121 36.798 1 64.14 ? H4' ADP 402 C 1 
HETATM 31 H H3' ADP . . . P 3 -35.47 -28.774 38.025 1 61.81 ? H3' ADP 402 C 1 
HETATM 32 H HO3' ADP . . . P 3 -35.137 -26.372 36.929 1 60.13 ? HO3' ADP 402 C 1 
HETATM 33 H H2' ADP . . . P 3 -36.048 -30.078 36.235 1 65.21 ? H2' ADP 402 C 1 
HETATM 34 H HO2' ADP . . . P 3 -35.563 -27.608 34.903 1 70.34 ? HO2' ADP 402 C 1 
HETATM 35 H H1' ADP . . . P 3 -34.169 -29.679 34.356 1 65.11 ? H1' ADP 402 C 1 
HETATM 36 H H8 ADP . . . P 3 -32.16 -30.988 37.257 1 63.5 ? H8 ADP 402 C 1 
HETATM 37 H HN61 ADP . . . P 3 -33.189 -36.709 34.722 1 55.14 ? HN61 ADP 402 C 1 
HETATM 38 H HN62 ADP . . . P 3 -32.313 -35.819 35.947 1 55.14 ? HN62 ADP 402 C 1 
HETATM 39 H H2 ADP . . . P 3 -35.75 -33.611 32.5 1 58.95 ? H2 ADP 402 C 1 
#
_model_server_stats.io_time_ms              49 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    43 
_model_server_stats.query_time_ms           289 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           39 
#