data_6YLA
#
_model_server_result.job_id            2ONUN7FjL_KNgs6FX--BMQ 
_model_server_result.datetime_utc      '2024-11-21 10:27:16' 
_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          6yla 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"JA","auth_seq_id":304}' 
#
_entry.id    6YLA 
#
_exptl.entry_id    6YLA 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              102.046 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'MALONATE ION' 
_entity.pdbx_number_of_molecules    12 
_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            6YLA 
_cell.length_a            163.124 
_cell.length_b            163.124 
_cell.length_c            189.076 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6YLA 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    'P 4abw 2nw' 
_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
? trimeric 3 author_defined_assembly 1 
? trimeric 3 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,MA,NA,OA 1 1 
D,E,F,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,PA,QA,RA 2 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
? 5 I N N 
? 5 N N N 
? 5 O N N 
? 5 R N N 
? 5 S N N 
? 5 BA N N 
? 5 CA N N 
? 5 DA N N 
? 5 EA N N 
? 5 JA N N 
? 5 KA N N 
? 5 LA 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 10 E CYS 336 1_555 A SG CYS 35 E CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf2 A SG CYS 53 E CYS 379 1_555 A SG CYS 106 E CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf3 A SG CYS 65 E CYS 391 1_555 A SG CYS 199 E CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf4 A SG CYS 154 E CYS 480 1_555 A SG CYS 162 E CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf5 B SG CYS 23 H CYS 22 1_555 B SG CYS 97 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf6 B SG CYS 145 H CYS 144 1_555 B SG CYS 201 H CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf7 C SG CYS 23 L CYS 23 1_555 C SG CYS 94 L CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf8 C SG CYS 140 L CYS 140 1_555 C SG CYS 200 L CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf9 D SG CYS 10 A CYS 336 1_555 D SG CYS 35 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf10 D SG CYS 53 A CYS 379 1_555 D SG CYS 106 A CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf11 D SG CYS 65 A CYS 391 1_555 D SG CYS 199 A CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf12 D SG CYS 154 A CYS 480 1_555 D SG CYS 162 A CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf13 E SG CYS 23 B CYS 22 1_555 E SG CYS 97 B CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf14 E SG CYS 145 B CYS 144 1_555 E SG CYS 201 B CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf15 F SG CYS 23 C CYS 23 1_555 F SG CYS 94 C CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf16 F SG CYS 140 C CYS 140 1_555 F SG CYS 200 C CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
covale ? covale1 A ND2 ASN 5 E ASN 331 1_555 L C1 NAG . E NAG 906 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? 
covale ? covale2 A ND2 ASN 17 E ASN 343 1_555 M C1 NAG . E NAG 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
covale ? covale3 D ND2 ASN 17 A ASN 343 1_555 Z C1 NAG . A NAG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? 
#
_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 283 n n 
C1 C3 MLI sing 284 n n 
C1 H11 MLI sing 285 n n 
C1 H12 MLI sing 286 n n 
C2 O6 MLI doub 287 n n 
C2 O7 MLI sing 288 n n 
C3 O8 MLI doub 289 n n 
C3 O9 MLI sing 290 n n 
#
_atom_sites.entry_id                     6YLA 
_atom_sites.fract_transf_matrix[1][1]    0.00613 
_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]    0.00613 
_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]    0.005289 
_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
G 4 DMS E 1 901 901 DMS DMS . 
H 4 DMS E 1 902 1001 DMS DMS . 
I 5 MLI E 1 903 1101 MLI MLI . 
J 4 DMS E 1 904 1201 DMS DMS . 
K 4 DMS E 1 905 1301 DMS DMS . 
L 6 NAG E 1 906 1401 NAG NAG . 
M 6 NAG E 1 907 1501 NAG NAG . 
N 5 MLI E 1 908 601 MLI MLI . 
O 5 MLI H 1 301 301 MLI MLI . 
P 4 DMS H 1 302 501 DMS DMS . 
Q 4 DMS H 1 303 701 DMS DMS . 
R 5 MLI H 1 304 801 MLI MLI . 
S 5 MLI H 1 305 901 MLI MLI . 
T 4 DMS L 1 1601 1601 DMS DMS . 
U 4 DMS L 1 1602 401 DMS DMS . 
V 7 1PE L 1 1603 301 1PE 1PE . 
W 4 DMS A 1 901 901 DMS DMS . 
X 8 PG0 A 1 902 1001 PG0 PG0 . 
Y 4 DMS A 1 903 1101 DMS DMS . 
Z 6 NAG A 1 904 1201 NAG NAG . 
AA 4 DMS A 1 905 1301 DMS DMS . 
BA 5 MLI B 1 301 301 MLI MLI . 
CA 5 MLI B 1 302 401 MLI MLI . 
DA 5 MLI B 1 303 501 MLI MLI . 
EA 5 MLI B 1 304 601 MLI MLI . 
FA 4 DMS B 1 305 401 DMS DMS . 
GA 7 1PE C 1 301 301 1PE 1PE . 
HA 4 DMS C 1 302 701 DMS DMS . 
IA 4 DMS C 1 303 801 DMS DMS . 
JA 5 MLI C 1 304 901 MLI MLI . 
KA 5 MLI C 1 305 1001 MLI MLI . 
LA 5 MLI C 1 306 1101 MLI MLI . 
MA 9 HOH E 1 1001 49 HOH HOH . 
MA 9 HOH E 2 1002 63 HOH HOH . 
MA 9 HOH E 3 1003 193 HOH HOH . 
MA 9 HOH E 4 1004 93 HOH HOH . 
MA 9 HOH E 5 1005 133 HOH HOH . 
MA 9 HOH E 6 1006 67 HOH HOH . 
NA 9 HOH H 1 401 59 HOH HOH . 
NA 9 HOH H 2 402 83 HOH HOH . 
NA 9 HOH H 3 403 65 HOH HOH . 
NA 9 HOH H 4 404 117 HOH HOH . 
NA 9 HOH H 5 405 120 HOH HOH . 
NA 9 HOH H 6 406 175 HOH HOH . 
NA 9 HOH H 7 407 148 HOH HOH . 
NA 9 HOH H 8 408 204 HOH HOH . 
NA 9 HOH H 9 409 205 HOH HOH . 
OA 9 HOH L 1 1701 77 HOH HOH . 
OA 9 HOH L 2 1702 149 HOH HOH . 
OA 9 HOH L 3 1703 110 HOH HOH . 
OA 9 HOH L 4 1704 112 HOH HOH . 
OA 9 HOH L 5 1705 103 HOH HOH . 
OA 9 HOH L 6 1706 163 HOH HOH . 
OA 9 HOH L 7 1707 166 HOH HOH . 
OA 9 HOH L 8 1708 98 HOH HOH . 
OA 9 HOH L 9 1709 16 HOH HOH . 
PA 9 HOH A 1 1001 203 HOH HOH . 
PA 9 HOH A 2 1002 45 HOH HOH . 
PA 9 HOH A 3 1003 168 HOH HOH . 
PA 9 HOH A 4 1004 207 HOH HOH . 
QA 9 HOH B 1 401 48 HOH HOH . 
QA 9 HOH B 2 402 186 HOH HOH . 
QA 9 HOH B 3 403 208 HOH HOH . 
QA 9 HOH B 4 404 108 HOH HOH . 
QA 9 HOH B 5 405 76 HOH HOH . 
QA 9 HOH B 6 406 206 HOH HOH . 
QA 9 HOH B 7 407 152 HOH HOH . 
QA 9 HOH B 8 408 146 HOH HOH . 
QA 9 HOH B 9 409 109 HOH HOH . 
QA 9 HOH B 10 410 104 HOH HOH . 
RA 9 HOH C 1 401 201 HOH HOH . 
RA 9 HOH C 2 402 56 HOH HOH . 
RA 9 HOH C 3 403 3 HOH HOH . 
RA 9 HOH C 4 404 47 HOH HOH . 
RA 9 HOH C 5 405 136 HOH HOH . 
RA 9 HOH C 6 406 92 HOH HOH . 
RA 9 HOH C 7 407 172 HOH HOH . 
RA 9 HOH C 8 408 95 HOH HOH . 
RA 9 HOH C 9 409 36 HOH HOH . 
RA 9 HOH C 10 410 147 HOH HOH . 
RA 9 HOH C 11 411 122 HOH HOH . 
RA 9 HOH C 12 412 142 HOH HOH . 
RA 9 HOH C 13 413 33 HOH HOH . 
RA 9 HOH C 14 414 29 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 . . . JA 5 43.705 -4.574 2.019 1 124.28 ? C1 MLI 304 C 1 
HETATM 2 C C2 MLI . . . JA 5 43.797 -3.062 1.835 1 127.58 ? C2 MLI 304 C 1 
HETATM 3 C C3 MLI . . . JA 5 42.616 -4.939 3.028 1 123.77 ? C3 MLI 304 C 1 
HETATM 4 O O6 MLI . . . JA 5 44.426 -2.573 0.859 1 129.04 ? O6 MLI 304 C 1 
HETATM 5 O O7 MLI . . . JA 5 43.245 -2.301 2.668 1 128.49 ? O7 MLI 304 C 1 
HETATM 6 O O8 MLI . . . JA 5 41.635 -5.646 2.672 1 123.7 ? O8 MLI 304 C 1 
HETATM 7 O O9 MLI . . . JA 5 42.714 -4.554 4.222 1 124.55 ? O9 MLI 304 C 1 
#
_model_server_stats.io_time_ms              34 
_model_server_stats.parse_time_ms           29 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           278 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           7 
#