data_5DBY
#
_model_server_result.job_id            b36NIOnjKM-3QZp5_Hbicg 
_model_server_result.datetime_utc      '2024-10-12 19:24:57' 
_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          5dby 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":605}' 
#
_entry.id    5DBY 
#
_exptl.entry_id    5DBY 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              102.046 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'MALONATE ION' 
_entity.pdbx_number_of_molecules    5 
_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            5DBY 
_cell.length_a            94.32 
_cell.length_b            94.32 
_cell.length_c            141.69 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5DBY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        169 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 61' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               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,S 
_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
? 4 D N N 
? 4 E N N 
? 4 F N N 
? 4 G N N 
? 4 H 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
disulf ? disulf1 A SG CYS 53 A CYS 53 1_555 A SG CYS 62 A CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? 
disulf ? disulf2 A SG CYS 75 A CYS 75 1_555 A SG CYS 91 A CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
disulf ? disulf3 A SG CYS 90 A CYS 90 1_555 A SG CYS 101 A CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? 
disulf ? disulf4 A SG CYS 123 A CYS 123 1_555 A SG CYS 168 A CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
disulf ? disulf5 A SG CYS 167 A CYS 167 1_555 A SG CYS 176 A CYS 176 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? 
disulf ? disulf6 A SG CYS 199 A CYS 199 1_555 A SG CYS 245 A CYS 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? 
disulf ? disulf7 A SG CYS 244 A CYS 244 1_555 A SG CYS 252 A CYS 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? 
disulf ? disulf8 A SG CYS 264 A CYS 264 1_555 A SG CYS 278 A CYS 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? 
disulf ? disulf9 A SG CYS 277 A CYS 277 1_555 A SG CYS 288 A CYS 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? 
disulf ? disulf10 A SG CYS 315 A CYS 315 1_555 A SG CYS 360 A CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf11 A SG CYS 359 A CYS 359 1_555 A SG CYS 368 A CYS 368 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? 
disulf ? disulf12 A SG CYS 391 A CYS 391 1_555 A SG CYS 437 A CYS 437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? 
disulf ? disulf13 A SG CYS 436 A CYS 436 1_555 A SG CYS 447 A CYS 447 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? 
disulf ? disulf14 A SG CYS 460 A CYS 460 1_555 A SG CYS 476 A CYS 476 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? 
disulf ? disulf15 A SG CYS 475 A CYS 475 1_555 A SG CYS 486 A CYS 486 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? 
disulf ? disulf16 A SG CYS 513 A CYS 513 1_555 A SG CYS 558 A CYS 558 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? 
disulf ? disulf17 A SG CYS 557 A CYS 557 1_555 A SG CYS 566 A CYS 566 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? 
#
_chem_comp.formula           'C3 H2 O4 -2' 
_chem_comp.formula_weight    102.046 
_chem_comp.id                MLI 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'MALONATE ION' 
_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
C1 C2 MLI sing 273 n n 
C1 C3 MLI sing 274 n n 
C1 H11 MLI sing 275 n n 
C1 H12 MLI sing 276 n n 
C2 O6 MLI doub 277 n n 
C2 O7 MLI sing 278 n n 
C3 O8 MLI doub 279 n n 
C3 O9 MLI sing 280 n n 
#
_atom_sites.entry_id                     5DBY 
_atom_sites.fract_transf_matrix[1][1]    0.010602 
_atom_sites.fract_transf_matrix[1][2]    0.006121 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012242 
_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]    0.007058 
_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 DIF A 1 601 1 DIF DIF . 
C 3 NPS A 1 602 1 NPS NPS . 
D 4 MLI A 1 603 1 MLI MLI . 
E 4 MLI A 1 604 2 MLI MLI . 
F 4 MLI A 1 605 3 MLI MLI . 
G 4 MLI A 1 606 4 MLI MLI . 
H 4 MLI A 1 607 5 MLI MLI . 
I 5 SIN A 1 608 6 SIN SIN . 
J 6 ACT A 1 609 7 ACT ACT . 
K 6 ACT A 1 610 8 ACT ACT . 
L 6 ACT A 1 611 9 ACT ACT . 
M 6 ACT A 1 612 10 ACT ACT . 
N 6 ACT A 1 613 11 ACT ACT . 
O 7 FMT A 1 614 12 FMT FMT . 
P 7 FMT A 1 615 14 FMT FMT . 
Q 8 LMR A 1 616 15 LMR LMR . 
R 6 ACT A 1 617 1 ACT ACT . 
S 9 HOH A 1 701 71 HOH HOH . 
S 9 HOH A 2 702 24 HOH HOH . 
S 9 HOH A 3 703 57 HOH HOH . 
S 9 HOH A 4 704 39 HOH HOH . 
S 9 HOH A 5 705 3 HOH HOH . 
S 9 HOH A 6 706 63 HOH HOH . 
S 9 HOH A 7 707 34 HOH HOH . 
S 9 HOH A 8 708 29 HOH HOH . 
S 9 HOH A 9 709 2 HOH HOH . 
S 9 HOH A 10 710 14 HOH HOH . 
S 9 HOH A 11 711 60 HOH HOH . 
S 9 HOH A 12 712 22 HOH HOH . 
S 9 HOH A 13 713 19 HOH HOH . 
S 9 HOH A 14 714 12 HOH HOH . 
S 9 HOH A 15 715 32 HOH HOH . 
S 9 HOH A 16 716 6 HOH HOH . 
S 9 HOH A 17 717 26 HOH HOH . 
S 9 HOH A 18 718 20 HOH HOH . 
S 9 HOH A 19 719 58 HOH HOH . 
S 9 HOH A 20 720 45 HOH HOH . 
S 9 HOH A 21 721 46 HOH HOH . 
S 9 HOH A 22 722 5 HOH HOH . 
S 9 HOH A 23 723 84 HOH HOH . 
S 9 HOH A 24 724 23 HOH HOH . 
S 9 HOH A 25 725 44 HOH HOH . 
S 9 HOH A 26 726 64 HOH HOH . 
S 9 HOH A 27 727 30 HOH HOH . 
S 9 HOH A 28 728 55 HOH HOH . 
S 9 HOH A 29 729 40 HOH HOH . 
S 9 HOH A 30 730 8 HOH HOH . 
S 9 HOH A 31 731 1 HOH HOH . 
S 9 HOH A 32 732 33 HOH HOH . 
S 9 HOH A 33 733 11 HOH HOH . 
S 9 HOH A 34 734 68 HOH HOH . 
S 9 HOH A 35 735 54 HOH HOH . 
S 9 HOH A 36 736 35 HOH HOH . 
S 9 HOH A 37 737 76 HOH HOH . 
S 9 HOH A 38 738 7 HOH HOH . 
S 9 HOH A 39 739 41 HOH HOH . 
S 9 HOH A 40 740 21 HOH HOH . 
S 9 HOH A 41 741 70 HOH HOH . 
S 9 HOH A 42 742 17 HOH HOH . 
S 9 HOH A 43 743 13 HOH HOH . 
S 9 HOH A 44 744 10 HOH HOH . 
S 9 HOH A 45 745 77 HOH HOH . 
S 9 HOH A 46 746 69 HOH HOH . 
S 9 HOH A 47 747 16 HOH HOH . 
S 9 HOH A 48 748 78 HOH HOH . 
S 9 HOH A 49 749 67 HOH HOH . 
S 9 HOH A 50 750 48 HOH HOH . 
S 9 HOH A 51 751 28 HOH HOH . 
S 9 HOH A 52 752 61 HOH HOH . 
S 9 HOH A 53 753 62 HOH HOH . 
S 9 HOH A 54 754 66 HOH HOH . 
S 9 HOH A 55 755 25 HOH HOH . 
S 9 HOH A 56 756 56 HOH HOH . 
S 9 HOH A 57 757 9 HOH HOH . 
S 9 HOH A 58 758 4 HOH HOH . 
S 9 HOH A 59 759 79 HOH HOH . 
S 9 HOH A 60 760 49 HOH HOH . 
S 9 HOH A 61 761 81 HOH HOH . 
S 9 HOH A 62 762 37 HOH HOH . 
S 9 HOH A 63 763 38 HOH HOH . 
S 9 HOH A 64 764 15 HOH HOH . 
S 9 HOH A 65 765 18 HOH HOH . 
S 9 HOH A 66 766 43 HOH HOH . 
S 9 HOH A 67 767 59 HOH HOH . 
S 9 HOH A 68 768 72 HOH HOH . 
S 9 HOH A 69 769 31 HOH HOH . 
S 9 HOH A 70 770 36 HOH HOH . 
S 9 HOH A 71 771 75 HOH HOH . 
S 9 HOH A 72 772 82 HOH HOH . 
S 9 HOH A 73 773 73 HOH HOH . 
S 9 HOH A 74 774 27 HOH HOH . 
S 9 HOH A 75 775 51 HOH HOH . 
S 9 HOH A 76 776 52 HOH HOH . 
S 9 HOH A 77 777 74 HOH HOH . 
S 9 HOH A 78 778 42 HOH HOH . 
S 9 HOH A 79 779 65 HOH HOH . 
S 9 HOH A 80 780 80 HOH HOH . 
S 9 HOH A 81 781 53 HOH HOH . 
S 9 HOH A 82 782 50 HOH HOH . 
S 9 HOH A 83 783 83 HOH HOH . 
S 9 HOH A 84 784 47 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 C C1 MLI . . . F 4 26.325 -8.055 57.046 1 68.11 ? C1 MLI 605 A 1 
HETATM 2 C C2 MLI . . . F 4 26.366 -6.622 56.565 1 69.12 ? C2 MLI 605 A 1 
HETATM 3 C C3 MLI . . . F 4 27.325 -8.977 56.392 1 63.27 ? C3 MLI 605 A 1 
HETATM 4 O O6 MLI . . . F 4 25.292 -6.127 56.136 1 74.76 ? O6 MLI 605 A 1 
HETATM 5 O O7 MLI . . . F 4 27.434 -5.972 56.64 1 66.62 ? O7 MLI 605 A 1 
HETATM 6 O O8 MLI . . . F 4 28.415 -8.569 55.983 1 58.93 ? O8 MLI 605 A 1 
HETATM 7 O O9 MLI . . . F 4 27.027 -10.181 56.316 1 67.59 ? O9 MLI 605 A 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           300 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           7 
#