data_6XV1
#
_model_server_result.job_id            UhFvNsQEtpLgdxd4g4KZ2w 
_model_server_result.datetime_utc      '2024-11-18 18:41:31' 
_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          6xv1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":401}' 
#
_entry.id    6XV1 
#
_exptl.entry_id    6XV1 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              559.316 
_entity.id                          2 
_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            6XV1 
_cell.length_a            91.175 
_cell.length_b            91.175 
_cell.length_c            143.584 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6XV1 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        173 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 63' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F,G,H,I,J,P 1 1 
B,K,L,M,N,O,Q 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
? 2 C N N 
? 2 K 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 135 A CYS 141 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? 
metalc ? metalc2 A SG CYS 138 A CYS 144 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
metalc ? metalc3 A SG CYS 160 A CYS 166 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? 
metalc ? metalc4 A SG CYS 171 A CYS 177 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? 
metalc ? metalc5 B SG CYS 135 B CYS 141 1_555 L ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? 
metalc ? metalc6 B SG CYS 138 B CYS 144 1_555 L ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? 
metalc ? metalc7 B SG CYS 160 B CYS 166 1_555 L ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? 
metalc ? metalc8 B SG CYS 171 B CYS 177 1_555 L ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.529 ? 
#
_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 63 n y 
N1 C6 AR6 sing 64 n y 
C2 N3 AR6 sing 65 n y 
N3 C4 AR6 doub 66 n y 
C4 C5 AR6 sing 67 n y 
C4 N9 AR6 sing 68 n y 
C5 C6 AR6 doub 69 n y 
C5 N7 AR6 sing 70 n y 
C6 N6 AR6 sing 71 n n 
N7 C8 AR6 doub 72 n y 
C8 N9 AR6 sing 73 n y 
N9 C1' AR6 sing 74 n n 
PA O1A AR6 sing 75 n n 
PA O2A AR6 doub 76 n n 
PA O3A AR6 sing 77 n n 
PA O5' AR6 sing 78 n n 
PB O1B AR6 sing 79 n n 
PB O2B AR6 doub 80 n n 
PB O3A AR6 sing 81 n n 
PB O5D AR6 sing 82 n n 
C1' C2' AR6 sing 83 n n 
C1' O4' AR6 sing 84 n n 
C1D O1D AR6 sing 85 n n 
C1D C2D AR6 sing 86 n n 
C1D O4D AR6 sing 87 n n 
C2' O2' AR6 sing 88 n n 
C2' C3' AR6 sing 89 n n 
C2D O2D AR6 sing 90 n n 
C2D C3D AR6 sing 91 n n 
C3' O3' AR6 sing 92 n n 
C3' C4' AR6 sing 93 n n 
C3D O3D AR6 sing 94 n n 
C3D C4D AR6 sing 95 n n 
C4' O4' AR6 sing 96 n n 
C4' C5' AR6 sing 97 n n 
C4D O4D AR6 sing 98 n n 
C4D C5D AR6 sing 99 n n 
C5' O5' AR6 sing 100 n n 
C5D O5D AR6 sing 101 n n 
C2 H2 AR6 sing 102 n n 
N6 HN6 AR6 sing 103 n n 
N6 HN6A AR6 sing 104 n n 
C8 H8 AR6 sing 105 n n 
C1' H1' AR6 sing 106 n n 
C1D H1D AR6 sing 107 n n 
C2' H2' AR6 sing 108 n n 
O2' HO2' AR6 sing 109 n n 
C2D H2D AR6 sing 110 n n 
O2D HO2D AR6 sing 111 n n 
C3' H3' AR6 sing 112 n n 
O3' HO3' AR6 sing 113 n n 
C3D H3D AR6 sing 114 n n 
O3D HO3D AR6 sing 115 n n 
C4' H4' AR6 sing 116 n n 
C4D H4D AR6 sing 117 n n 
C5' H5' AR6 sing 118 n n 
C5' "H5'A" AR6 sing 119 n n 
C5D H5D AR6 sing 120 n n 
C5D H5DA AR6 sing 121 n n 
O1A H1A AR6 sing 122 n n 
O1B H1B AR6 sing 123 n n 
O1D HD1 AR6 sing 124 n n 
#
_atom_sites.entry_id                     6XV1 
_atom_sites.fract_transf_matrix[1][1]    0.010968 
_atom_sites.fract_transf_matrix[1][2]    0.006332 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012665 
_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]    0.006965 
_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 AR6 A 1 401 500 AR6 AR6 . 
D 3 ZN A 1 402 501 ZN ZN . 
E 4 8L9 A 1 403 601 8L9 LIG . 
F 5 SO4 A 1 404 3 SO4 SO4 . 
G 5 SO4 A 1 405 4 SO4 SO4 . 
H 5 SO4 A 1 406 6 SO4 SO4 . 
I 5 SO4 A 1 407 7 SO4 SO4 . 
J 5 SO4 A 1 408 8 SO4 SO4 . 
K 2 AR6 B 1 401 500 AR6 AR6 . 
L 3 ZN B 1 402 501 ZN ZN . 
M 5 SO4 B 1 403 1 SO4 SO4 . 
N 5 SO4 B 1 404 2 SO4 SO4 . 
O 5 SO4 B 1 405 5 SO4 SO4 . 
P 6 HOH A 1 501 33 HOH HOH . 
P 6 HOH A 2 502 11 HOH HOH . 
P 6 HOH A 3 503 71 HOH HOH . 
P 6 HOH A 4 504 57 HOH HOH . 
P 6 HOH A 5 505 22 HOH HOH . 
P 6 HOH A 6 506 30 HOH HOH . 
P 6 HOH A 7 507 63 HOH HOH . 
P 6 HOH A 8 508 32 HOH HOH . 
P 6 HOH A 9 509 15 HOH HOH . 
P 6 HOH A 10 510 75 HOH HOH . 
P 6 HOH A 11 511 53 HOH HOH . 
P 6 HOH A 12 512 46 HOH HOH . 
P 6 HOH A 13 513 21 HOH HOH . 
P 6 HOH A 14 514 1 HOH HOH . 
P 6 HOH A 15 515 76 HOH HOH . 
P 6 HOH A 16 516 41 HOH HOH . 
P 6 HOH A 17 517 45 HOH HOH . 
P 6 HOH A 18 518 37 HOH HOH . 
P 6 HOH A 19 519 70 HOH HOH . 
P 6 HOH A 20 520 8 HOH HOH . 
P 6 HOH A 21 521 23 HOH HOH . 
P 6 HOH A 22 522 67 HOH HOH . 
P 6 HOH A 23 523 17 HOH HOH . 
P 6 HOH A 24 524 84 HOH HOH . 
P 6 HOH A 25 525 27 HOH HOH . 
P 6 HOH A 26 526 24 HOH HOH . 
P 6 HOH A 27 527 12 HOH HOH . 
P 6 HOH A 28 528 60 HOH HOH . 
P 6 HOH A 29 529 10 HOH HOH . 
P 6 HOH A 30 530 3 HOH HOH . 
P 6 HOH A 31 531 40 HOH HOH . 
P 6 HOH A 32 532 44 HOH HOH . 
P 6 HOH A 33 533 31 HOH HOH . 
P 6 HOH A 34 534 2 HOH HOH . 
P 6 HOH A 35 535 39 HOH HOH . 
P 6 HOH A 36 536 25 HOH HOH . 
P 6 HOH A 37 537 14 HOH HOH . 
P 6 HOH A 38 538 74 HOH HOH . 
P 6 HOH A 39 539 51 HOH HOH . 
P 6 HOH A 40 540 35 HOH HOH . 
P 6 HOH A 41 541 77 HOH HOH . 
P 6 HOH A 42 542 52 HOH HOH . 
P 6 HOH A 43 543 73 HOH HOH . 
P 6 HOH A 44 544 26 HOH HOH . 
P 6 HOH A 45 545 20 HOH HOH . 
P 6 HOH A 46 546 62 HOH HOH . 
P 6 HOH A 47 547 56 HOH HOH . 
P 6 HOH A 48 548 43 HOH HOH . 
P 6 HOH A 49 549 69 HOH HOH . 
P 6 HOH A 50 550 29 HOH HOH . 
P 6 HOH A 51 551 61 HOH HOH . 
P 6 HOH A 52 552 58 HOH HOH . 
P 6 HOH A 53 553 80 HOH HOH . 
P 6 HOH A 54 554 82 HOH HOH . 
P 6 HOH A 55 555 81 HOH HOH . 
P 6 HOH A 56 556 78 HOH HOH . 
Q 6 HOH B 1 501 86 HOH HOH . 
Q 6 HOH B 2 502 85 HOH HOH . 
Q 6 HOH B 3 503 87 HOH HOH . 
Q 6 HOH B 4 504 36 HOH HOH . 
Q 6 HOH B 5 505 16 HOH HOH . 
Q 6 HOH B 6 506 66 HOH HOH . 
Q 6 HOH B 7 507 65 HOH HOH . 
Q 6 HOH B 8 508 18 HOH HOH . 
Q 6 HOH B 9 509 64 HOH HOH . 
Q 6 HOH B 10 510 59 HOH HOH . 
Q 6 HOH B 11 511 5 HOH HOH . 
Q 6 HOH B 12 512 48 HOH HOH . 
Q 6 HOH B 13 513 42 HOH HOH . 
Q 6 HOH B 14 514 54 HOH HOH . 
Q 6 HOH B 15 515 34 HOH HOH . 
Q 6 HOH B 16 516 55 HOH HOH . 
Q 6 HOH B 17 517 9 HOH HOH . 
Q 6 HOH B 18 518 49 HOH HOH . 
Q 6 HOH B 19 519 13 HOH HOH . 
Q 6 HOH B 20 520 7 HOH HOH . 
Q 6 HOH B 21 521 50 HOH HOH . 
Q 6 HOH B 22 522 68 HOH HOH . 
Q 6 HOH B 23 523 4 HOH HOH . 
Q 6 HOH B 24 524 6 HOH HOH . 
Q 6 HOH B 25 525 72 HOH HOH . 
Q 6 HOH B 26 526 83 HOH HOH . 
Q 6 HOH B 27 527 47 HOH HOH . 
Q 6 HOH B 28 528 38 HOH HOH . 
Q 6 HOH B 29 529 19 HOH HOH . 
Q 6 HOH B 30 530 28 HOH HOH . 
Q 6 HOH B 31 531 79 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 . . . K 2 -19.545 24.717 37.091 1 29.35 ? N1 AR6 401 B 1 
HETATM 2 C C2 AR6 . . . K 2 -19.736 25.585 38.087 1 30.96 ? C2 AR6 401 B 1 
HETATM 3 N N3 AR6 . . . K 2 -20.847 25.822 38.784 1 27.02 ? N3 AR6 401 B 1 
HETATM 4 C C4 AR6 . . . K 2 -21.851 25.073 38.288 1 28.26 ? C4 AR6 401 B 1 
HETATM 5 C C5 AR6 . . . K 2 -21.791 24.113 37.276 1 28.69 ? C5 AR6 401 B 1 
HETATM 6 C C6 AR6 . . . K 2 -20.57 23.987 36.59 1 30.38 ? C6 AR6 401 B 1 
HETATM 7 N N6 AR6 . . . K 2 -20.316 23.073 35.622 1 28.33 ? N6 AR6 401 B 1 
HETATM 8 N N7 AR6 . . . K 2 -23.03 23.505 37.1 1 30.37 ? N7 AR6 401 B 1 
HETATM 9 C C8 AR6 . . . K 2 -23.82 24.08 37.993 1 31.19 ? C8 AR6 401 B 1 
HETATM 10 N N9 AR6 . . . K 2 -23.106 24.996 38.796 1 30.49 ? N9 AR6 401 B 1 
HETATM 11 P PA AR6 . . . K 2 -27.424 23.91 44.035 1 36.24 ? PA AR6 401 B 1 
HETATM 12 P PB AR6 . . . K 2 -26.222 22.097 45.966 1 34.09 ? PB AR6 401 B 1 
HETATM 13 C C1' AR6 . . . K 2 -23.514 25.678 39.963 1 31.33 ? C1' AR6 401 B 1 
HETATM 14 O O1A AR6 . . . K 2 -27.9 24.582 45.311 1 39.2 ? O1A AR6 401 B 1 
HETATM 15 O O1B AR6 . . . K 2 -25.418 20.822 45.93 1 36.3 ? O1B AR6 401 B 1 
HETATM 16 C C1D AR6 . . . K 2 -30.684 20.342 47.591 1 39.81 ? C1D AR6 401 B 1 
HETATM 17 O O1D AR6 . . . K 2 -31.832 20.49 48.278 1 44.85 ? O1D AR6 401 B 1 
HETATM 18 C C2' AR6 . . . K 2 -24.837 26.365 39.838 1 26.61 ? C2' AR6 401 B 1 
HETATM 19 O O2' AR6 . . . K 2 -24.644 27.694 39.422 1 30.03 ? O2' AR6 401 B 1 
HETATM 20 O O2A AR6 . . . K 2 -28.301 23.638 42.86 1 36.16 ? O2A AR6 401 B 1 
HETATM 21 O O2B AR6 . . . K 2 -25.52 23.335 46.396 1 36.1 ? O2B AR6 401 B 1 
HETATM 22 C C2D AR6 . . . K 2 -30.129 18.934 47.787 1 37.08 ? C2D AR6 401 B 1 
HETATM 23 O O2D AR6 . . . K 2 -30.414 18.457 49.078 1 43.22 ? O2D AR6 401 B 1 
HETATM 24 C C3' AR6 . . . K 2 -25.355 26.34 41.282 1 27.6 ? C3' AR6 401 B 1 
HETATM 25 O O3' AR6 . . . K 2 -25.005 27.64 41.719 1 26 ? O3' AR6 401 B 1 
HETATM 26 O O3A AR6 . . . K 2 -26.947 22.444 44.558 1 34.61 ? O3A AR6 401 B 1 
HETATM 27 C C3D AR6 . . . K 2 -28.633 19.126 47.665 1 38.4 ? C3D AR6 401 B 1 
HETATM 28 O O3D AR6 . . . K 2 -27.995 18.049 48.338 1 39.65 ? O3D AR6 401 B 1 
HETATM 29 C C4' AR6 . . . K 2 -24.575 25.206 41.958 1 26.99 ? C4' AR6 401 B 1 
HETATM 30 O O4' AR6 . . . K 2 -23.683 24.688 40.951 1 29.8 ? O4' AR6 401 B 1 
HETATM 31 C C4D AR6 . . . K 2 -28.504 20.449 48.439 1 35.88 ? C4D AR6 401 B 1 
HETATM 32 O O4D AR6 . . . K 2 -29.66 21.223 48.062 1 39.97 ? O4D AR6 401 B 1 
HETATM 33 C C5' AR6 . . . K 2 -25.381 24.069 42.495 1 32.74 ? C5' AR6 401 B 1 
HETATM 34 O O5' AR6 . . . K 2 -26.111 24.621 43.595 1 36.24 ? O5' AR6 401 B 1 
HETATM 35 C C5D AR6 . . . K 2 -27.303 21.267 48.168 1 36.22 ? C5D AR6 401 B 1 
HETATM 36 O O5D AR6 . . . K 2 -27.479 21.874 46.864 1 33.85 ? O5D AR6 401 B 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           38 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           309 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           36 
#