data_5HNR
#
_model_server_result.job_id            kfRWzaqoM6Sz63NVyNUEmw 
_model_server_result.datetime_utc      '2024-10-13 10:21:42' 
_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          5hnr 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":503}' 
#
_entry.id    5HNR 
#
_exptl.entry_id    5HNR 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              118.154 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'DELTA-AMINO VALERIC ACID' 
_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            5HNR 
_cell.length_a            125.53 
_cell.length_b            125.53 
_cell.length_c            200.91 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5HNR 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        97 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 4 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    octameric 
_pdbx_struct_assembly.oligomeric_count      8 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3,4 
#
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_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 125.53 125.53 0 
3 'crystal symmetry operation' 3_655 -y+1,x,z 0 -1 0 1 0 0 0 0 1 125.53 0 0 
4 'crystal symmetry operation' 4_565 y,-x+1,z 0 1 0 -1 0 0 0 0 1 0 125.53 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             E 
_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
covale ? covale1 A NZ LYS 252 A LYS 252 1_555 E CG DAV . A DAV 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.52 ? 
metalc ? metalc1 A SG CYS 122 A CYS 122 1_555 C ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? 
metalc ? metalc2 A SG CYS 124 A CYS 124 1_555 C ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? 
metalc ? metalc3 A SG CYS 132 A CYS 132 1_555 C ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? 
metalc ? metalc4 C ZN ZN . A ZN 501 1_555 G O HOH . A HOH 662 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
#
_chem_comp.formula           'C5 H12 N O2 1' 
_chem_comp.formula_weight    118.154 
_chem_comp.id                DAV 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'DELTA-AMINO VALERIC ACID' 
_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
OXT C DAV sing 83 n n 
OXT HXT DAV sing 84 n n 
O C DAV doub 85 n n 
CB CG DAV sing 86 n n 
CB C1 DAV sing 87 n n 
CB HCB1 DAV sing 88 n n 
CB HCB2 DAV sing 89 n n 
CG CD DAV sing 90 n n 
CG HCG1 DAV sing 91 n n 
CG HCG2 DAV sing 92 n n 
CD N DAV sing 93 n n 
CD HCD1 DAV sing 94 n n 
CD HCD2 DAV sing 95 n n 
N H DAV sing 96 n n 
N H2 DAV sing 97 n n 
N H3 DAV sing 98 n n 
C C1 DAV sing 99 n n 
C1 HCA1 DAV sing 100 n n 
C1 HCA2 DAV sing 101 n n 
#
_atom_sites.entry_id                     5HNR 
_atom_sites.fract_transf_matrix[1][1]    0.007966 
_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]    0.007966 
_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]    0.004977 
_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 ZN A 1 501 501 ZN ZN . 
D 3 SO4 A 1 502 502 SO4 SO4 . 
E 4 DAV A 1 503 600 DAV DAV . 
F 3 SO4 B 1 401 503 SO4 SO4 . 
G 5 HOH A 1 601 57 HOH HOH . 
G 5 HOH A 2 602 28 HOH HOH . 
G 5 HOH A 3 603 7 HOH HOH . 
G 5 HOH A 4 604 40 HOH HOH . 
G 5 HOH A 5 605 13 HOH HOH . 
G 5 HOH A 6 606 47 HOH HOH . 
G 5 HOH A 7 607 6 HOH HOH . 
G 5 HOH A 8 608 43 HOH HOH . 
G 5 HOH A 9 609 5 HOH HOH . 
G 5 HOH A 10 610 121 HOH HOH . 
G 5 HOH A 11 611 98 HOH HOH . 
G 5 HOH A 12 612 59 HOH HOH . 
G 5 HOH A 13 613 52 HOH HOH . 
G 5 HOH A 14 614 49 HOH HOH . 
G 5 HOH A 15 615 16 HOH HOH . 
G 5 HOH A 16 616 102 HOH HOH . 
G 5 HOH A 17 617 24 HOH HOH . 
G 5 HOH A 18 618 41 HOH HOH . 
G 5 HOH A 19 619 18 HOH HOH . 
G 5 HOH A 20 620 14 HOH HOH . 
G 5 HOH A 21 621 11 HOH HOH . 
G 5 HOH A 22 622 8 HOH HOH . 
G 5 HOH A 23 623 17 HOH HOH . 
G 5 HOH A 24 624 51 HOH HOH . 
G 5 HOH A 25 625 55 HOH HOH . 
G 5 HOH A 26 626 33 HOH HOH . 
G 5 HOH A 27 627 93 HOH HOH . 
G 5 HOH A 28 628 21 HOH HOH . 
G 5 HOH A 29 629 83 HOH HOH . 
G 5 HOH A 30 630 97 HOH HOH . 
G 5 HOH A 31 631 22 HOH HOH . 
G 5 HOH A 32 632 99 HOH HOH . 
G 5 HOH A 33 633 31 HOH HOH . 
G 5 HOH A 34 634 68 HOH HOH . 
G 5 HOH A 35 635 108 HOH HOH . 
G 5 HOH A 36 636 76 HOH HOH . 
G 5 HOH A 37 637 53 HOH HOH . 
G 5 HOH A 38 638 62 HOH HOH . 
G 5 HOH A 39 639 118 HOH HOH . 
G 5 HOH A 40 640 44 HOH HOH . 
G 5 HOH A 41 641 50 HOH HOH . 
G 5 HOH A 42 642 123 HOH HOH . 
G 5 HOH A 43 643 58 HOH HOH . 
G 5 HOH A 44 644 106 HOH HOH . 
G 5 HOH A 45 645 35 HOH HOH . 
G 5 HOH A 46 646 103 HOH HOH . 
G 5 HOH A 47 647 115 HOH HOH . 
G 5 HOH A 48 648 82 HOH HOH . 
G 5 HOH A 49 649 65 HOH HOH . 
G 5 HOH A 50 650 75 HOH HOH . 
G 5 HOH A 51 651 20 HOH HOH . 
G 5 HOH A 52 652 91 HOH HOH . 
G 5 HOH A 53 653 79 HOH HOH . 
G 5 HOH A 54 654 101 HOH HOH . 
G 5 HOH A 55 655 113 HOH HOH . 
G 5 HOH A 56 656 29 HOH HOH . 
G 5 HOH A 57 657 73 HOH HOH . 
G 5 HOH A 58 658 9 HOH HOH . 
G 5 HOH A 59 659 86 HOH HOH . 
G 5 HOH A 60 660 3 HOH HOH . 
G 5 HOH A 61 661 92 HOH HOH . 
G 5 HOH A 62 662 550 HOH HOH . 
G 5 HOH A 63 663 122 HOH HOH . 
G 5 HOH A 64 664 117 HOH HOH . 
G 5 HOH A 65 665 88 HOH HOH . 
G 5 HOH A 66 666 70 HOH HOH . 
G 5 HOH A 67 667 120 HOH HOH . 
G 5 HOH A 68 668 2 HOH HOH . 
G 5 HOH A 69 669 89 HOH HOH . 
G 5 HOH A 70 670 116 HOH HOH . 
G 5 HOH A 71 671 119 HOH HOH . 
G 5 HOH A 72 672 114 HOH HOH . 
G 5 HOH A 73 673 4 HOH HOH . 
G 5 HOH A 74 674 100 HOH HOH . 
H 5 HOH B 1 501 109 HOH HOH . 
H 5 HOH B 2 502 54 HOH HOH . 
H 5 HOH B 3 503 26 HOH HOH . 
H 5 HOH B 4 504 61 HOH HOH . 
H 5 HOH B 5 505 95 HOH HOH . 
H 5 HOH B 6 506 45 HOH HOH . 
H 5 HOH B 7 507 12 HOH HOH . 
H 5 HOH B 8 508 78 HOH HOH . 
H 5 HOH B 9 509 37 HOH HOH . 
H 5 HOH B 10 510 19 HOH HOH . 
H 5 HOH B 11 511 10 HOH HOH . 
H 5 HOH B 12 512 69 HOH HOH . 
H 5 HOH B 13 513 96 HOH HOH . 
H 5 HOH B 14 514 111 HOH HOH . 
H 5 HOH B 15 515 32 HOH HOH . 
H 5 HOH B 16 516 23 HOH HOH . 
H 5 HOH B 17 517 36 HOH HOH . 
H 5 HOH B 18 518 15 HOH HOH . 
H 5 HOH B 19 519 74 HOH HOH . 
H 5 HOH B 20 520 39 HOH HOH . 
H 5 HOH B 21 521 27 HOH HOH . 
H 5 HOH B 22 522 30 HOH HOH . 
H 5 HOH B 23 523 72 HOH HOH . 
H 5 HOH B 24 524 81 HOH HOH . 
H 5 HOH B 25 525 34 HOH HOH . 
H 5 HOH B 26 526 87 HOH HOH . 
H 5 HOH B 27 527 105 HOH HOH . 
H 5 HOH B 28 528 80 HOH HOH . 
H 5 HOH B 29 529 90 HOH HOH . 
H 5 HOH B 30 530 38 HOH HOH . 
H 5 HOH B 31 531 42 HOH HOH . 
H 5 HOH B 32 532 1 HOH HOH . 
H 5 HOH B 33 533 64 HOH HOH . 
H 5 HOH B 34 534 25 HOH HOH . 
H 5 HOH B 35 535 84 HOH HOH . 
H 5 HOH B 36 536 110 HOH HOH . 
H 5 HOH B 37 537 56 HOH HOH . 
H 5 HOH B 38 538 77 HOH HOH . 
H 5 HOH B 39 539 104 HOH HOH . 
H 5 HOH B 40 540 107 HOH HOH . 
H 5 HOH B 41 541 124 HOH HOH . 
H 5 HOH B 42 542 112 HOH HOH . 
H 5 HOH B 43 543 46 HOH HOH . 
H 5 HOH B 44 544 48 HOH HOH . 
H 5 HOH B 45 545 94 HOH HOH . 
H 5 HOH B 46 546 85 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 OXT DAV . . . E 4 29.008 74.399 53.903 1 53.69 ? OXT DAV 503 A 1 
HETATM 2 O O DAV . . . E 4 29.196 72.219 53.738 1 50.41 ? O DAV 503 A 1 
HETATM 3 C CB DAV . . . E 4 31.055 72.581 55.919 1 76.92 ? CB DAV 503 A 1 
HETATM 4 C CG DAV . . . E 4 32.28 72.677 56.795 1 78.57 ? CG DAV 503 A 1 
HETATM 5 C CD DAV . . . E 4 32.388 73.109 58.265 1 90.02 ? CD DAV 503 A 1 
HETATM 6 N N DAV . . . E 4 32.914 72.057 59.168 1 96.99 ? N DAV 503 A 1 
HETATM 7 C C DAV . . . E 4 29.599 73.339 54.1 1 56.29 ? C DAV 503 A 1 
HETATM 8 C C1 DAV . . . E 4 30.944 73.516 54.727 1 65.47 ? C1 DAV 503 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           27 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           274 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           8 
#