data_2ZI4
#
_model_server_result.job_id            F03LrUePhLcRy3uFI0Z7Yg 
_model_server_result.datetime_utc      '2024-10-16 10:28:43' 
_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          2zi4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":401}' 
#
_entry.id    2ZI4 
#
_exptl.entry_id    2ZI4 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              251.242 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (2S,3R,5S)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol 
_entity.pdbx_number_of_molecules    1 
_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            2ZI4 
_cell.length_a            79.73 
_cell.length_b            79.73 
_cell.length_c            93.53 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2ZI4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
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' 8_555 -y,-x,-z+1/2 0 -1 0 -1 0 0 0 0 -1 0 0 46.765 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 OG SER 54 A SER 35 1_555 B MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? 
metalc ? metalc2 A OE1 GLU 146 A GLU 127 1_555 B MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? 
metalc ? metalc3 D O1B ADP . A ADP 301 1_555 B MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? 
metalc ? metalc4 B MG MG . A MG 501 1_555 E O HOH . A HOH 551 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? 
#
_chem_comp.formula           'C10 H13 N5 O3' 
_chem_comp.formula_weight    251.242 
_chem_comp.id                3L1 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (2S,3R,5S)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "L-2'-deoxyadenosine" 
#
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
N6 C6 3L1 sing 1 n n 
C6 N1 3L1 doub 2 n y 
C6 C5 3L1 sing 3 n y 
N1 C2 3L1 sing 4 n y 
C2 N3 3L1 doub 5 n y 
N3 C4 3L1 sing 6 n y 
C4 C5 3L1 doub 7 n y 
C4 N9 3L1 sing 8 n y 
C5 N7 3L1 sing 9 n y 
N7 C8 3L1 doub 10 n y 
C8 N9 3L1 sing 11 n y 
N9 C1' 3L1 sing 12 n n 
C1' O4' 3L1 sing 13 n n 
C1' C2' 3L1 sing 14 n n 
O4' C4' 3L1 sing 15 n n 
C2' C3' 3L1 sing 16 n n 
C3' O3' 3L1 sing 17 n n 
C3' C4' 3L1 sing 18 n n 
C4' C5' 3L1 sing 19 n n 
C5' O5' 3L1 sing 20 n n 
N6 HN6 3L1 sing 21 n n 
N6 HN6A 3L1 sing 22 n n 
C2 H2 3L1 sing 23 n n 
C8 H8 3L1 sing 24 n n 
C1' H1' 3L1 sing 25 n n 
C2' H2' 3L1 sing 26 n n 
C2' "H2'A" 3L1 sing 27 n n 
C3' H3' 3L1 sing 28 n n 
O3' HO3' 3L1 sing 29 n n 
C4' H4' 3L1 sing 30 n n 
C5' H5' 3L1 sing 31 n n 
C5' "H5'A" 3L1 sing 32 n n 
O5' HO5' 3L1 sing 33 n n 
#
_atom_sites.entry_id                     2ZI4 
_atom_sites.fract_transf_matrix[1][1]    0.012542 
_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]    0.012542 
_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]    0.010692 
_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
B 2 MG A 1 501 501 MG MG . 
C 3 3L1 A 1 401 401 3L1 LAD . 
D 4 ADP A 1 301 301 ADP ADP . 
E 5 HOH A 1 502 1 HOH HOH . 
E 5 HOH A 2 503 2 HOH HOH . 
E 5 HOH A 3 504 3 HOH HOH . 
E 5 HOH A 4 505 4 HOH HOH . 
E 5 HOH A 5 506 5 HOH HOH . 
E 5 HOH A 6 507 6 HOH HOH . 
E 5 HOH A 7 508 7 HOH HOH . 
E 5 HOH A 8 509 8 HOH HOH . 
E 5 HOH A 9 510 9 HOH HOH . 
E 5 HOH A 10 511 10 HOH HOH . 
E 5 HOH A 11 512 11 HOH HOH . 
E 5 HOH A 12 513 12 HOH HOH . 
E 5 HOH A 13 514 13 HOH HOH . 
E 5 HOH A 14 515 14 HOH HOH . 
E 5 HOH A 15 516 15 HOH HOH . 
E 5 HOH A 16 517 16 HOH HOH . 
E 5 HOH A 17 518 17 HOH HOH . 
E 5 HOH A 18 519 18 HOH HOH . 
E 5 HOH A 19 520 19 HOH HOH . 
E 5 HOH A 20 521 20 HOH HOH . 
E 5 HOH A 21 522 21 HOH HOH . 
E 5 HOH A 22 523 22 HOH HOH . 
E 5 HOH A 23 524 23 HOH HOH . 
E 5 HOH A 24 525 24 HOH HOH . 
E 5 HOH A 25 526 26 HOH HOH . 
E 5 HOH A 26 527 27 HOH HOH . 
E 5 HOH A 27 528 29 HOH HOH . 
E 5 HOH A 28 529 30 HOH HOH . 
E 5 HOH A 29 530 31 HOH HOH . 
E 5 HOH A 30 531 32 HOH HOH . 
E 5 HOH A 31 532 33 HOH HOH . 
E 5 HOH A 32 533 34 HOH HOH . 
E 5 HOH A 33 534 35 HOH HOH . 
E 5 HOH A 34 535 37 HOH HOH . 
E 5 HOH A 35 536 38 HOH HOH . 
E 5 HOH A 36 537 40 HOH HOH . 
E 5 HOH A 37 538 41 HOH HOH . 
E 5 HOH A 38 539 42 HOH HOH . 
E 5 HOH A 39 540 43 HOH HOH . 
E 5 HOH A 40 541 44 HOH HOH . 
E 5 HOH A 41 542 45 HOH HOH . 
E 5 HOH A 42 543 46 HOH HOH . 
E 5 HOH A 43 544 47 HOH HOH . 
E 5 HOH A 44 545 48 HOH HOH . 
E 5 HOH A 45 546 49 HOH HOH . 
E 5 HOH A 46 547 50 HOH HOH . 
E 5 HOH A 47 548 51 HOH HOH . 
E 5 HOH A 48 549 52 HOH HOH . 
E 5 HOH A 49 550 53 HOH HOH . 
E 5 HOH A 50 551 54 HOH HOH . 
E 5 HOH A 51 552 55 HOH HOH . 
E 5 HOH A 52 553 56 HOH HOH . 
E 5 HOH A 53 554 57 HOH HOH . 
E 5 HOH A 54 555 58 HOH HOH . 
E 5 HOH A 55 556 59 HOH HOH . 
E 5 HOH A 56 557 60 HOH HOH . 
E 5 HOH A 57 558 62 HOH HOH . 
E 5 HOH A 58 559 63 HOH HOH . 
E 5 HOH A 59 560 64 HOH HOH . 
E 5 HOH A 60 561 66 HOH HOH . 
E 5 HOH A 61 562 67 HOH HOH . 
E 5 HOH A 62 563 68 HOH HOH . 
E 5 HOH A 63 564 69 HOH HOH . 
E 5 HOH A 64 565 70 HOH HOH . 
E 5 HOH A 65 566 71 HOH HOH . 
E 5 HOH A 66 567 72 HOH HOH . 
E 5 HOH A 67 568 73 HOH HOH . 
E 5 HOH A 68 569 75 HOH HOH . 
E 5 HOH A 69 570 76 HOH HOH . 
E 5 HOH A 70 571 77 HOH HOH . 
E 5 HOH A 71 572 78 HOH HOH . 
E 5 HOH A 72 573 79 HOH HOH . 
E 5 HOH A 73 574 80 HOH HOH . 
E 5 HOH A 74 575 81 HOH HOH . 
E 5 HOH A 75 576 82 HOH HOH . 
E 5 HOH A 76 577 83 HOH HOH . 
E 5 HOH A 77 578 84 HOH HOH . 
E 5 HOH A 78 579 85 HOH HOH . 
E 5 HOH A 79 580 86 HOH HOH . 
E 5 HOH A 80 581 87 HOH HOH . 
E 5 HOH A 81 582 88 HOH HOH . 
E 5 HOH A 82 583 89 HOH HOH . 
E 5 HOH A 83 584 90 HOH HOH . 
E 5 HOH A 84 585 91 HOH HOH . 
E 5 HOH A 85 586 92 HOH HOH . 
E 5 HOH A 86 587 93 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 N6 3L1 . . . C 3 23.53 -7.609 17.984 1 18.37 ? N6 3L1 401 A 1 
HETATM 2 C C6 3L1 . . . C 3 24.79 -7.813 18.149 1 18.73 ? C6 3L1 401 A 1 
HETATM 3 N N1 3L1 . . . C 3 25.438 -8.942 17.957 1 18.24 ? N1 3L1 401 A 1 
HETATM 4 C C2 3L1 . . . C 3 26.834 -9.218 18.103 1 18.59 ? C2 3L1 401 A 1 
HETATM 5 N N3 3L1 . . . C 3 27.617 -8.098 18.494 1 16.53 ? N3 3L1 401 A 1 
HETATM 6 C C4 3L1 . . . C 3 26.981 -6.9 18.708 1 18.3 ? C4 3L1 401 A 1 
HETATM 7 C C5 3L1 . . . C 3 25.659 -6.705 18.547 1 17.75 ? C5 3L1 401 A 1 
HETATM 8 N N7 3L1 . . . C 3 25.385 -5.418 18.857 1 19.89 ? N7 3L1 401 A 1 
HETATM 9 C C8 3L1 . . . C 3 26.597 -4.837 19.158 1 17.77 ? C8 3L1 401 A 1 
HETATM 10 N N9 3L1 . . . C 3 27.595 -5.791 19.062 1 19.57 ? N9 3L1 401 A 1 
HETATM 11 C C1' 3L1 . . . C 3 29.007 -5.653 19.34 1 19.15 ? C1' 3L1 401 A 1 
HETATM 12 O O4' 3L1 . . . C 3 29.237 -4.266 19.58 1 23.13 ? O4' 3L1 401 A 1 
HETATM 13 C C2' 3L1 . . . C 3 29.362 -6.297 20.654 1 22.67 ? C2' 3L1 401 A 1 
HETATM 14 C C3' 3L1 . . . C 3 30.59 -5.502 21.056 1 23.43 ? C3' 3L1 401 A 1 
HETATM 15 O O3' 3L1 . . . C 3 31.792 -6.068 20.554 1 23.22 ? O3' 3L1 401 A 1 
HETATM 16 C C4' 3L1 . . . C 3 30.45 -4.159 20.347 1 22.05 ? C4' 3L1 401 A 1 
HETATM 17 C C5' 3L1 . . . C 3 30.392 -2.997 21.327 1 23.24 ? C5' 3L1 401 A 1 
HETATM 18 O O5' 3L1 . . . C 3 29.781 -1.809 20.785 1 25.19 ? O5' 3L1 401 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           268 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           18 
#