data_8I2B
#
_model_server_result.job_id            ZSKLn6lZ1bxGabLu03OAuA 
_model_server_result.datetime_utc      '2024-11-26 11:38:50' 
_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          8i2b 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":604}' 
#
_entry.id    8I2B 
#
_exptl.entry_id    8I2B 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              559.316 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE' 
_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         120 
_cell.entry_id            8I2B 
_cell.length_a            91.318 
_cell.length_b            91.318 
_cell.length_c            143.674 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8I2B 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        173 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 63' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3 
#
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' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 
3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 E N N 
? 4 J 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 SG CYS 133 A CYS 141 1_555 F ZN ZN . A ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? 
metalc ? metalc2 A SG CYS 136 A CYS 144 1_555 F ZN ZN . A ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? 
metalc ? metalc3 A SG CYS 158 A CYS 166 1_555 F ZN ZN . A ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? 
metalc ? metalc4 A SG CYS 169 A CYS 177 1_555 F ZN ZN . A ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.489 ? 
metalc ? metalc5 B SG CYS 133 B CYS 141 1_555 K ZN ZN . B ZN 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? 
metalc ? metalc6 B SG CYS 136 B CYS 144 1_555 K ZN ZN . B ZN 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? 
metalc ? metalc7 B SG CYS 158 B CYS 166 1_555 K ZN ZN . B ZN 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? 
metalc ? metalc8 B SG CYS 169 B CYS 177 1_555 K ZN ZN . B ZN 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.927 ? 
#
_chem_comp.formula           'C15 H23 N5 O14 P2' 
_chem_comp.formula_weight    559.316 
_chem_comp.id                AR6 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     Adenosine-5-Diphosphoribose 
#
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
N1 C2 AR6 doub 13 n y 
N1 C6 AR6 sing 14 n y 
C2 N3 AR6 sing 15 n y 
N3 C4 AR6 doub 16 n y 
C4 C5 AR6 sing 17 n y 
C4 N9 AR6 sing 18 n y 
C5 C6 AR6 doub 19 n y 
C5 N7 AR6 sing 20 n y 
C6 N6 AR6 sing 21 n n 
N7 C8 AR6 doub 22 n y 
C8 N9 AR6 sing 23 n y 
N9 C1' AR6 sing 24 n n 
PA O1A AR6 sing 25 n n 
PA O2A AR6 doub 26 n n 
PA O3A AR6 sing 27 n n 
PA O5' AR6 sing 28 n n 
PB O1B AR6 sing 29 n n 
PB O2B AR6 doub 30 n n 
PB O3A AR6 sing 31 n n 
PB O5D AR6 sing 32 n n 
C1' C2' AR6 sing 33 n n 
C1' O4' AR6 sing 34 n n 
C1D O1D AR6 sing 35 n n 
C1D C2D AR6 sing 36 n n 
C1D O4D AR6 sing 37 n n 
C2' O2' AR6 sing 38 n n 
C2' C3' AR6 sing 39 n n 
C2D O2D AR6 sing 40 n n 
C2D C3D AR6 sing 41 n n 
C3' O3' AR6 sing 42 n n 
C3' C4' AR6 sing 43 n n 
C3D O3D AR6 sing 44 n n 
C3D C4D AR6 sing 45 n n 
C4' O4' AR6 sing 46 n n 
C4' C5' AR6 sing 47 n n 
C4D O4D AR6 sing 48 n n 
C4D C5D AR6 sing 49 n n 
C5' O5' AR6 sing 50 n n 
C5D O5D AR6 sing 51 n n 
C2 H2 AR6 sing 52 n n 
N6 HN6 AR6 sing 53 n n 
N6 HN6A AR6 sing 54 n n 
C8 H8 AR6 sing 55 n n 
C1' H1' AR6 sing 56 n n 
C1D H1D AR6 sing 57 n n 
C2' H2' AR6 sing 58 n n 
O2' HO2' AR6 sing 59 n n 
C2D H2D AR6 sing 60 n n 
O2D HO2D AR6 sing 61 n n 
C3' H3' AR6 sing 62 n n 
O3' HO3' AR6 sing 63 n n 
C3D H3D AR6 sing 64 n n 
O3D HO3D AR6 sing 65 n n 
C4' H4' AR6 sing 66 n n 
C4D H4D AR6 sing 67 n n 
C5' H5' AR6 sing 68 n n 
C5' "H5'A" AR6 sing 69 n n 
C5D H5D AR6 sing 70 n n 
C5D H5DA AR6 sing 71 n n 
O1A H1A AR6 sing 72 n n 
O1B H1B AR6 sing 73 n n 
O1D HD1 AR6 sing 74 n n 
#
_atom_sites.entry_id                     8I2B 
_atom_sites.fract_transf_matrix[1][1]    0.010951 
_atom_sites.fract_transf_matrix[1][2]    0.006322 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012645 
_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]    0.00696 
_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
C 2 PG4 A 1 401 401 PG4 PG4 . 
D 3 O5L A 1 402 501 O5L UNL . 
E 4 AR6 A 1 403 701 AR6 AR6 . 
F 5 ZN A 1 404 2 ZN ZN . 
G 2 PG4 B 1 601 601 PG4 PG4 . 
H 2 PG4 B 1 602 401 PG4 PG4 . 
I 3 O5L B 1 603 501 O5L UNL . 
J 4 AR6 B 1 604 601 AR6 AR6 . 
K 5 ZN B 1 605 1 ZN ZN . 
L 6 SO4 B 1 606 1 SO4 SO4 . 
M 6 SO4 B 1 607 2 SO4 SO4 . 
N 6 SO4 B 1 608 3 SO4 SO4 . 
O 6 SO4 B 1 609 4 SO4 SO4 . 
P 6 SO4 B 1 610 5 SO4 SO4 . 
Q 7 HOH A 1 501 35 HOH HOH . 
Q 7 HOH A 2 502 53 HOH HOH . 
Q 7 HOH A 3 503 16 HOH HOH . 
Q 7 HOH A 4 504 18 HOH HOH . 
Q 7 HOH A 5 505 55 HOH HOH . 
Q 7 HOH A 6 506 47 HOH HOH . 
Q 7 HOH A 7 507 26 HOH HOH . 
Q 7 HOH A 8 508 21 HOH HOH . 
Q 7 HOH A 9 509 32 HOH HOH . 
Q 7 HOH A 10 510 23 HOH HOH . 
Q 7 HOH A 11 511 36 HOH HOH . 
Q 7 HOH A 12 512 62 HOH HOH . 
Q 7 HOH A 13 513 25 HOH HOH . 
Q 7 HOH A 14 514 56 HOH HOH . 
Q 7 HOH A 15 515 39 HOH HOH . 
Q 7 HOH A 16 516 60 HOH HOH . 
Q 7 HOH A 17 517 17 HOH HOH . 
Q 7 HOH A 18 518 40 HOH HOH . 
Q 7 HOH A 19 519 50 HOH HOH . 
Q 7 HOH A 20 520 43 HOH HOH . 
Q 7 HOH A 21 521 58 HOH HOH . 
Q 7 HOH A 22 522 54 HOH HOH . 
Q 7 HOH A 23 523 22 HOH HOH . 
Q 7 HOH A 24 524 33 HOH HOH . 
Q 7 HOH A 25 525 24 HOH HOH . 
Q 7 HOH A 26 526 52 HOH HOH . 
Q 7 HOH A 27 527 19 HOH HOH . 
Q 7 HOH A 28 528 45 HOH HOH . 
Q 7 HOH A 29 529 46 HOH HOH . 
Q 7 HOH A 30 530 44 HOH HOH . 
Q 7 HOH A 31 531 20 HOH HOH . 
Q 7 HOH A 32 532 49 HOH HOH . 
Q 7 HOH A 33 533 59 HOH HOH . 
Q 7 HOH A 34 534 48 HOH HOH . 
Q 7 HOH A 35 535 37 HOH HOH . 
Q 7 HOH A 36 536 61 HOH HOH . 
Q 7 HOH A 37 537 57 HOH HOH . 
Q 7 HOH A 38 538 34 HOH HOH . 
Q 7 HOH A 39 539 51 HOH HOH . 
R 7 HOH B 1 701 74 HOH HOH . 
R 7 HOH B 2 702 77 HOH HOH . 
R 7 HOH B 3 703 6 HOH HOH . 
R 7 HOH B 4 704 71 HOH HOH . 
R 7 HOH B 5 705 70 HOH HOH . 
R 7 HOH B 6 706 13 HOH HOH . 
R 7 HOH B 7 707 63 HOH HOH . 
R 7 HOH B 8 708 8 HOH HOH . 
R 7 HOH B 9 709 2 HOH HOH . 
R 7 HOH B 10 710 76 HOH HOH . 
R 7 HOH B 11 711 11 HOH HOH . 
R 7 HOH B 12 712 4 HOH HOH . 
R 7 HOH B 13 713 38 HOH HOH . 
R 7 HOH B 14 714 69 HOH HOH . 
R 7 HOH B 15 715 3 HOH HOH . 
R 7 HOH B 16 716 5 HOH HOH . 
R 7 HOH B 17 717 42 HOH HOH . 
R 7 HOH B 18 718 41 HOH HOH . 
R 7 HOH B 19 719 68 HOH HOH . 
R 7 HOH B 20 720 10 HOH HOH . 
R 7 HOH B 21 721 12 HOH HOH . 
R 7 HOH B 22 722 9 HOH HOH . 
R 7 HOH B 23 723 14 HOH HOH . 
R 7 HOH B 24 724 27 HOH HOH . 
R 7 HOH B 25 725 67 HOH HOH . 
R 7 HOH B 26 726 30 HOH HOH . 
R 7 HOH B 27 727 65 HOH HOH . 
R 7 HOH B 28 728 7 HOH HOH . 
R 7 HOH B 29 729 28 HOH HOH . 
R 7 HOH B 30 730 15 HOH HOH . 
R 7 HOH B 31 731 66 HOH HOH . 
R 7 HOH B 32 732 78 HOH HOH . 
R 7 HOH B 33 733 75 HOH HOH . 
R 7 HOH B 34 734 73 HOH HOH . 
R 7 HOH B 35 735 64 HOH HOH . 
R 7 HOH B 36 736 72 HOH HOH . 
R 7 HOH B 37 737 79 HOH HOH . 
R 7 HOH B 38 738 80 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 N N1 AR6 . . . J 4 -19.444 24.781 36.997 1 37.67 ? N1 AR6 604 B 1 
HETATM 2 C C2 AR6 . . . J 4 -19.624 25.672 37.986 1 44.12 ? C2 AR6 604 B 1 
HETATM 3 N N3 AR6 . . . J 4 -20.713 25.932 38.703 1 37.52 ? N3 AR6 604 B 1 
HETATM 4 C C4 AR6 . . . J 4 -21.751 25.192 38.267 1 38.4 ? C4 AR6 604 B 1 
HETATM 5 C C5 AR6 . . . J 4 -21.735 24.287 37.234 1 33.27 ? C5 AR6 604 B 1 
HETATM 6 C C6 AR6 . . . J 4 -20.5 24.056 36.581 1 36.01 ? C6 AR6 604 B 1 
HETATM 7 N N6 AR6 . . . J 4 -20.297 23.179 35.592 1 38.08 ? N6 AR6 604 B 1 
HETATM 8 N N7 AR6 . . . J 4 -23.013 23.766 37.072 1 39.86 ? N7 AR6 604 B 1 
HETATM 9 C C8 AR6 . . . J 4 -23.756 24.361 37.982 1 36.16 ? C8 AR6 604 B 1 
HETATM 10 N N9 AR6 . . . J 4 -23.053 25.263 38.697 1 40.41 ? N9 AR6 604 B 1 
HETATM 11 P PA AR6 . . . J 4 -27.326 23.955 43.947 1 46.39 ? PA AR6 604 B 1 
HETATM 12 P PB AR6 . . . J 4 -26.164 22.304 45.944 1 44.67 ? PB AR6 604 B 1 
HETATM 13 C C1' AR6 . . . J 4 -23.512 25.997 39.873 1 37.8 ? C1' AR6 604 B 1 
HETATM 14 O O1A AR6 . . . J 4 -28.022 24.735 45.011 1 54.25 ? O1A AR6 604 B 1 
HETATM 15 O O1B AR6 . . . J 4 -25.341 21.071 45.895 1 42.85 ? O1B AR6 604 B 1 
HETATM 16 C C1D AR6 . . . J 4 -30.783 20.559 47.542 1 53.17 ? C1D AR6 604 B 1 
HETATM 17 O O1D AR6 . . . J 4 -31.968 20.71 48.238 1 59.43 ? O1D AR6 604 B 1 
HETATM 18 C C2' AR6 . . . J 4 -24.865 26.685 39.85 1 39.39 ? C2' AR6 604 B 1 
HETATM 19 O O2' AR6 . . . J 4 -24.637 27.985 39.343 1 39.25 ? O2' AR6 604 B 1 
HETATM 20 O O2A AR6 . . . J 4 -28.076 23.641 42.699 1 47.8 ? O2A AR6 604 B 1 
HETATM 21 O O2B AR6 . . . J 4 -25.478 23.55 46.348 1 42.63 ? O2B AR6 604 B 1 
HETATM 22 C C2D AR6 . . . J 4 -30.259 19.129 47.671 1 54.47 ? C2D AR6 604 B 1 
HETATM 23 O O2D AR6 . . . J 4 -30.53 18.55 48.921 1 53.89 ? O2D AR6 604 B 1 
HETATM 24 C C3' AR6 . . . J 4 -25.262 26.668 41.343 1 38.01 ? C3' AR6 604 B 1 
HETATM 25 O O3' AR6 . . . J 4 -24.94 27.873 42.034 1 39.01 ? O3' AR6 604 B 1 
HETATM 26 O O3A AR6 . . . J 4 -26.825 22.569 44.534 1 51.15 ? O3A AR6 604 B 1 
HETATM 27 C C3D AR6 . . . J 4 -28.756 19.322 47.519 1 52.41 ? C3D AR6 604 B 1 
HETATM 28 O O3D AR6 . . . J 4 -28.073 18.223 48.102 1 50.24 ? O3D AR6 604 B 1 
HETATM 29 C C4' AR6 . . . J 4 -24.449 25.507 41.945 1 34.05 ? C4' AR6 604 B 1 
HETATM 30 O O4' AR6 . . . J 4 -23.658 25.011 40.859 1 32.87 ? O4' AR6 604 B 1 
HETATM 31 C C4D AR6 . . . J 4 -28.573 20.59 48.353 1 48.68 ? C4D AR6 604 B 1 
HETATM 32 O O4D AR6 . . . J 4 -29.762 21.384 48.107 1 50.15 ? O4D AR6 604 B 1 
HETATM 33 C C5' AR6 . . . J 4 -25.242 24.339 42.445 1 41.49 ? C5' AR6 604 B 1 
HETATM 34 O O5' AR6 . . . J 4 -26.005 24.755 43.584 1 43.18 ? O5' AR6 604 B 1 
HETATM 35 C C5D AR6 . . . J 4 -27.348 21.42 48.087 1 43.34 ? C5D AR6 604 B 1 
HETATM 36 O O5D AR6 . . . J 4 -27.468 22.069 46.806 1 42.11 ? O5D AR6 604 B 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           312 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           36 
#