data_5EEL
#
_model_server_result.job_id            6JLRMGNc5gzaSAGF7XJdMg 
_model_server_result.datetime_utc      '2024-11-29 15:57:50' 
_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          5eel 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"U","auth_seq_id":601}' 
#
_entry.id    5EEL 
#
_exptl.entry_id    5EEL 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              104.061 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'MALONIC ACID' 
_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         90 
_cell.entry_id            5EEL 
_cell.length_a            95.228 
_cell.length_b            95.228 
_cell.length_c            241.566 
_cell.Z_PDB               48 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5EEL 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
PISA dimeric 2 author_and_software_defined_assembly 4 
PISA dimeric 2 author_and_software_defined_assembly 5 
PISA dimeric 2 author_and_software_defined_assembly 6 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,H,M,N,O,DA 1 1 
B,I,P,Q,EA,KA 2 1 
C,J,R,S,T,FA 3 1 
D,K,U,V,W,GA 4 1 
E,L,X,Y,Z,HA,LA 5 1 
F,G,AA,BA,CA,IA,JA 6 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
? 3 M N N 
? 3 R N N 
? 3 U N N 
? 3 X N N 
? 3 AA 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 G N SER 1 L SER 1 1_555 G C5 AEA 9 L AEA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.421 ? 
covale ? covale2 G OG SER 1 L SER 1 1_555 G C4 73C 8 L 73C 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.4 ? 
covale ? covale3 G C ASN 7 L ASN 7 1_555 G N 73C 8 L 73C 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.315 ? 
covale ? covale4 G C 73C 8 L 73C 8 1_555 G N1 AEA 9 L AEA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.415 ? 
covale ? covale5 H N SER 1 M SER 1 1_555 H C5 AEA 9 M AEA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.414 ? 
covale ? covale6 H OG SER 1 M SER 1 1_555 H C4 73C 8 M 73C 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.398 ? 
covale ? covale7 H C ASN 7 M ASN 7 1_555 H N 73C 8 M 73C 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? 
covale ? covale8 H C 73C 8 M 73C 8 1_555 H N1 AEA 9 M AEA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.403 ? 
covale ? covale9 I N SER 1 N SER 1 1_555 I C5 AEA 9 N AEA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? 
covale ? covale10 I OG SER 1 N SER 1 1_555 I C4 73C 8 N 73C 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.396 ? 
covale ? covale11 I C ASN 7 N ASN 7 1_555 I N 73C 8 N 73C 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? 
covale ? covale12 I C 73C 8 N 73C 8 1_555 I N1 AEA 9 N AEA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.416 ? 
covale ? covale13 J OG SER 1 P SER 1 1_555 J C4 73C 8 P 73C 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.401 ? 
covale ? covale14 J C ASN 7 P ASN 7 1_555 J N 73C 8 P 73C 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? 
covale ? covale15 K N SER 1 Q SER 1 1_555 K C5 AEA 9 Q AEA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.416 ? 
covale ? covale16 K OG SER 1 Q SER 1 1_555 K C4 73C 8 Q 73C 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.402 ? 
covale ? covale17 K C ASN 7 Q ASN 7 1_555 K N 73C 8 Q 73C 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? 
covale ? covale18 K C 73C 8 Q 73C 8 1_555 K N1 AEA 9 Q AEA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.408 ? 
covale ? covale19 L N SER 1 R SER 1 1_555 L C5 AEA 9 R AEA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.39 ? 
covale ? covale20 L OG SER 1 R SER 1 1_555 L C4 73C 8 R 73C 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.405 ? 
covale ? covale21 L C ASN 7 R ASN 7 1_555 L N 73C 8 R 73C 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale22 L C 73C 8 R 73C 8 1_555 L N1 AEA 9 R AEA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.408 ? 
metalc ? metalc1 N O2 FMT . A FMT 602 1_555 O NA NA . A NA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.927 ? 
metalc ? metalc2 P O2 FMT . B FMT 601 1_555 Q NA NA . B NA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.92 ? 
metalc ? metalc3 S O2 FMT . C FMT 602 1_555 T NA NA . C NA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.929 ? 
metalc ? metalc4 V O2 FMT . D FMT 602 1_555 W NA NA . D NA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.934 ? 
metalc ? metalc5 Y O2 FMT . E FMT 602 1_555 Z NA NA . E NA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.928 ? 
metalc ? metalc6 BA O2 FMT . F FMT 602 1_555 CA NA NA . F NA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.934 ? 
#
_chem_comp.formula           'C3 H4 O4' 
_chem_comp.formula_weight    104.061 
_chem_comp.id                MLA 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'MALONIC ACID' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'DICARBOXYLIC ACID C3;PROPANEDIOLIC ACID;METHANEDICARBOXYLIC ACID' 
#
_atom_sites.entry_id                     5EEL 
_atom_sites.fract_transf_matrix[1][1]    0.010501 
_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]    0.010501 
_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]    0.00414 
_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
M 3 MLA A 1 601 3 MLA MLA . 
N 4 FMT A 1 602 2 FMT FMT . 
O 5 NA A 1 603 8 NA NA . 
P 4 FMT B 1 601 3 FMT FMT . 
Q 5 NA B 1 602 9 NA NA . 
R 3 MLA C 1 601 4 MLA MLA . 
S 4 FMT C 1 602 4 FMT FMT . 
T 5 NA C 1 603 10 NA NA . 
U 3 MLA D 1 601 6 MLA MLA . 
V 4 FMT D 1 602 5 FMT FMT . 
W 5 NA D 1 603 11 NA NA . 
X 3 MLA E 1 601 2 MLA MLA . 
Y 4 FMT E 1 602 1 FMT FMT . 
Z 5 NA E 1 603 7 NA NA . 
AA 3 MLA F 1 601 5 MLA MLA . 
BA 4 FMT F 1 602 6 FMT FMT . 
CA 5 NA F 1 603 12 NA NA . 
DA 6 HOH A 1 701 16 HOH HOH . 
DA 6 HOH A 2 702 44 HOH HOH . 
DA 6 HOH A 3 703 29 HOH HOH . 
DA 6 HOH A 4 704 30 HOH HOH . 
DA 6 HOH A 5 705 48 HOH HOH . 
DA 6 HOH A 6 706 20 HOH HOH . 
EA 6 HOH B 1 701 4 HOH HOH . 
EA 6 HOH B 2 702 21 HOH HOH . 
EA 6 HOH B 3 703 25 HOH HOH . 
EA 6 HOH B 4 704 60 HOH HOH . 
EA 6 HOH B 5 705 1 HOH HOH . 
EA 6 HOH B 6 706 74 HOH HOH . 
EA 6 HOH B 7 707 7 HOH HOH . 
EA 6 HOH B 8 708 55 HOH HOH . 
EA 6 HOH B 9 709 64 HOH HOH . 
EA 6 HOH B 10 710 36 HOH HOH . 
EA 6 HOH B 11 711 12 HOH HOH . 
EA 6 HOH B 12 712 34 HOH HOH . 
EA 6 HOH B 13 713 27 HOH HOH . 
EA 6 HOH B 14 714 22 HOH HOH . 
EA 6 HOH B 15 715 69 HOH HOH . 
EA 6 HOH B 16 716 42 HOH HOH . 
EA 6 HOH B 17 717 28 HOH HOH . 
EA 6 HOH B 18 718 61 HOH HOH . 
EA 6 HOH B 19 719 66 HOH HOH . 
EA 6 HOH B 20 720 24 HOH HOH . 
EA 6 HOH B 21 721 47 HOH HOH . 
EA 6 HOH B 22 722 35 HOH HOH . 
FA 6 HOH C 1 701 56 HOH HOH . 
GA 6 HOH D 1 701 11 HOH HOH . 
GA 6 HOH D 2 702 5 HOH HOH . 
GA 6 HOH D 3 703 15 HOH HOH . 
GA 6 HOH D 4 704 31 HOH HOH . 
GA 6 HOH D 5 705 51 HOH HOH . 
GA 6 HOH D 6 706 67 HOH HOH . 
HA 6 HOH E 1 701 63 HOH HOH . 
HA 6 HOH E 2 702 14 HOH HOH . 
HA 6 HOH E 3 703 71 HOH HOH . 
HA 6 HOH E 4 704 3 HOH HOH . 
HA 6 HOH E 5 705 26 HOH HOH . 
HA 6 HOH E 6 706 10 HOH HOH . 
HA 6 HOH E 7 707 8 HOH HOH . 
HA 6 HOH E 8 708 46 HOH HOH . 
HA 6 HOH E 9 709 32 HOH HOH . 
HA 6 HOH E 10 710 6 HOH HOH . 
IA 6 HOH F 1 701 19 HOH HOH . 
IA 6 HOH F 2 702 17 HOH HOH . 
IA 6 HOH F 3 703 2 HOH HOH . 
IA 6 HOH F 4 704 58 HOH HOH . 
IA 6 HOH F 5 705 54 HOH HOH . 
IA 6 HOH F 6 706 50 HOH HOH . 
IA 6 HOH F 7 707 53 HOH HOH . 
IA 6 HOH F 8 708 72 HOH HOH . 
IA 6 HOH F 9 709 18 HOH HOH . 
IA 6 HOH F 10 710 57 HOH HOH . 
IA 6 HOH F 11 711 23 HOH HOH . 
IA 6 HOH F 12 712 43 HOH HOH . 
IA 6 HOH F 13 713 75 HOH HOH . 
IA 6 HOH F 14 714 13 HOH HOH . 
IA 6 HOH F 15 715 73 HOH HOH . 
IA 6 HOH F 16 716 38 HOH HOH . 
IA 6 HOH F 17 717 33 HOH HOH . 
IA 6 HOH F 18 718 65 HOH HOH . 
IA 6 HOH F 19 719 41 HOH HOH . 
IA 6 HOH F 20 720 49 HOH HOH . 
IA 6 HOH F 21 721 37 HOH HOH . 
IA 6 HOH F 22 722 68 HOH HOH . 
JA 6 HOH L 1 101 45 HOH HOH . 
JA 6 HOH L 2 102 40 HOH HOH . 
JA 6 HOH L 3 103 9 HOH HOH . 
JA 6 HOH L 4 104 59 HOH HOH . 
KA 6 HOH N 1 101 39 HOH HOH . 
KA 6 HOH N 2 102 62 HOH HOH . 
KA 6 HOH N 3 103 70 HOH HOH . 
LA 6 HOH R 1 101 52 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 MLA . . . U 3 47.406 16.744 49.849 1 42.17 ? C1 MLA 601 D 1 
HETATM 2 O O1A MLA . . . U 3 47.065 17.36 50.9 1 40.51 ? O1A MLA 601 D 1 
HETATM 3 O O1B MLA . . . U 3 48.136 15.713 49.903 1 42.62 ? O1B MLA 601 D 1 
HETATM 4 C C2 MLA . . . U 3 46.97 17.234 48.491 1 34.16 ? C2 MLA 601 D 1 
HETATM 5 C C3 MLA . . . U 3 48.185 17.324 47.595 1 45.51 ? C3 MLA 601 D 1 
HETATM 6 O O3A MLA . . . U 3 48.336 16.548 46.607 1 49.27 ? O3A MLA 601 D 1 
HETATM 7 O O3B MLA . . . U 3 49.064 18.184 47.855 1 43.8 ? O3B MLA 601 D 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    27 
_model_server_stats.query_time_ms           327 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           7 
#