data_2Z3K
#
_model_server_result.job_id            YPx5cDuNpkTa-IYCUIo2Zg 
_model_server_result.datetime_utc      '2024-11-23 19:19:06' 
_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          2z3k 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":401}' 
#
_entry.id    2Z3K 
#
_exptl.entry_id    2Z3K 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              267.241 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-(6-AMINO-OCTAHYDRO-PURIN-9-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL 
_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            2Z3K 
_cell.length_a            115.106 
_cell.length_b            129.846 
_cell.length_c            38.691 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2Z3K 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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
? 2 C N N 
? 2 F 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
covale ? covale1 C O3' XYA . A XYA 301 1_555 D C PHE . A PHE 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale2 F O3' XYA . B XYA 401 1_555 G C PHE . B PHE 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? 
#
_chem_comp.formula           'C10 H13 N5 O4' 
_chem_comp.formula_weight    267.241 
_chem_comp.id                XYA 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-(6-AMINO-OCTAHYDRO-PURIN-9-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     9-BETA-D-XYLOFURANOSYL-ADENINE 
#
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
O5' C5' XYA sing 391 n n 
O5' H5' XYA sing 392 n n 
C5' C4' XYA sing 393 n n 
C5' "H5'1" XYA sing 394 n n 
C5' "H5'2" XYA sing 395 n n 
C4' O4' XYA sing 396 n n 
C4' C3' XYA sing 397 n n 
C4' H4' XYA sing 398 n n 
O4' C1' XYA sing 399 n n 
C1' N9 XYA sing 400 n n 
C1' C2' XYA sing 401 n n 
C1' H1' XYA sing 402 n n 
N9 C8 XYA sing 403 n y 
N9 C4 XYA sing 404 n y 
C8 N7 XYA doub 405 n y 
C8 H8 XYA sing 406 n n 
N7 C5 XYA sing 407 n y 
C5 C6 XYA doub 408 n y 
C5 C4 XYA sing 409 n y 
C6 N1 XYA sing 410 n y 
C6 N6 XYA sing 411 n n 
N1 C2 XYA doub 412 n y 
C2 N3 XYA sing 413 n y 
C2 H2 XYA sing 414 n n 
N3 C4 XYA doub 415 n y 
N6 HN61 XYA sing 416 n n 
N6 HN62 XYA sing 417 n n 
C2' O2' XYA sing 418 n n 
C2' C3' XYA sing 419 n n 
C2' H2' XYA sing 420 n n 
O2' H1 XYA sing 421 n n 
C3' O3' XYA sing 422 n n 
C3' H3' XYA sing 423 n n 
O3' H3 XYA sing 424 n n 
#
_atom_sites.entry_id                     2Z3K 
_atom_sites.fract_transf_matrix[1][1]    0.008688 
_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]    0.007701 
_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]    0.025846 
_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 XYA A 1 301 301 XYA XYA . 
D 3 PHE A 1 302 302 PHE PHE . 
E 4 TAR A 1 501 501 TAR TAR . 
F 2 XYA B 1 401 401 XYA XYA . 
G 3 PHE B 1 402 402 PHE PHE . 
H 4 TAR B 1 502 502 TAR TAR . 
I 5 HOH A 1 1002 1002 HOH HOH . 
I 5 HOH A 2 1003 1003 HOH HOH . 
I 5 HOH A 3 1006 1006 HOH HOH . 
I 5 HOH A 4 1007 1007 HOH HOH . 
I 5 HOH A 5 1009 1009 HOH HOH . 
J 5 HOH B 1 1001 1001 HOH HOH . 
J 5 HOH B 2 1004 1004 HOH HOH . 
J 5 HOH B 3 1005 1005 HOH HOH . 
J 5 HOH B 4 1008 1008 HOH HOH . 
J 5 HOH B 5 1010 1010 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 O O5' XYA . . . F 2 9.271 19.129 21.845 1 135.62 ? O5' XYA 401 B 1 
HETATM 2 C C5' XYA . . . F 2 10.268 18.934 22.846 1 138.03 ? C5' XYA 401 B 1 
HETATM 3 C C4' XYA . . . F 2 11.504 19.732 22.508 1 138.02 ? C4' XYA 401 B 1 
HETATM 4 O O4' XYA . . . F 2 12.469 19.644 23.598 1 140.55 ? O4' XYA 401 B 1 
HETATM 5 C C1' XYA . . . F 2 13.781 19.857 23.079 1 141.35 ? C1' XYA 401 B 1 
HETATM 6 N N9 XYA . . . F 2 14.635 18.706 23.375 1 159.96 ? N9 XYA 401 B 1 
HETATM 7 C C8 XYA . . . F 2 14.39 17.586 24.131 1 160.6 ? C8 XYA 401 B 1 
HETATM 8 N N7 XYA . . . F 2 15.375 16.717 24.124 1 160.8 ? N7 XYA 401 B 1 
HETATM 9 C C5 XYA . . . F 2 16.339 17.311 23.319 1 161.36 ? C5 XYA 401 B 1 
HETATM 10 C C6 XYA . . . F 2 17.621 16.891 22.899 1 161.66 ? C6 XYA 401 B 1 
HETATM 11 N N1 XYA . . . F 2 18.322 17.727 22.098 1 161.82 ? N1 XYA 401 B 1 
HETATM 12 C C2 XYA . . . F 2 17.767 18.898 21.745 1 161.66 ? C2 XYA 401 B 1 
HETATM 13 N N3 XYA . . . F 2 16.575 19.397 22.069 1 161.39 ? N3 XYA 401 B 1 
HETATM 14 C C4 XYA . . . F 2 15.903 18.544 22.866 1 161.04 ? C4 XYA 401 B 1 
HETATM 15 N N6 XYA . . . F 2 18.173 15.72 23.243 1 161.17 ? N6 XYA 401 B 1 
HETATM 16 C C2' XYA . . . F 2 13.639 19.964 21.562 1 139.73 ? C2' XYA 401 B 1 
HETATM 17 O O2' XYA . . . F 2 13.583 21.31 21.157 1 141.43 ? O2' XYA 401 B 1 
HETATM 18 C C3' XYA . . . F 2 12.322 19.244 21.326 1 138.08 ? C3' XYA 401 B 1 
HETATM 19 O O3' XYA . . . F 2 11.81 19.599 20.083 1 135.55 ? O3' XYA 401 B 1 
#
_model_server_stats.io_time_ms              44 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           294 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           19 
#