data_6C1R
#
_model_server_result.job_id            7kq-312NjNRNxlYopWuOOA 
_model_server_result.datetime_utc      '2024-11-27 06:08:27' 
_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          6c1r 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":502}' 
#
_entry.id    6C1R 
#
_exptl.entry_id    6C1R 
_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    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          106.08 
_cell.angle_gamma         90 
_cell.entry_id            6C1R 
_cell.length_a            58.411 
_cell.length_b            52.608 
_cell.length_c            83.865 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6C1R 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_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,F,G,H,I,J,K,L,M,N,O 
_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 
#
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 195 B CYS 195 1_555 A SG CYS 274 B CYS 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
covale ? covale1 A C TRP 229 B TRP 229 1_555 A N YCM 230 B YCM 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale2 A C YCM 230 B YCM 230 1_555 A N GLN 231 B GLN 231 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale3 B C ACE 1 L ACE 0 1_555 B N PHE 2 L PHE 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale4 B C PHE 2 L PHE 1 1_555 B N ORN 3 L ORN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale5 B C ORN 3 L ORN 2 1_555 B N PRO 4 L PRO 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? 
covale ? covale6 B NE ORN 3 L ORN 2 1_555 B C ARG 7 L ARG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale7 B C PRO 4 L PRO 3 1_555 B N ZAL 5 L ZAL 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale8 B C ZAL 5 L ZAL 4 1_555 B N TRP 6 L TRP 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
metalc ? metalc1 A OD2 ASP 168 B ASP 168 1_555 F NA NA . B NA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.726 ? 
metalc ? metalc2 A O ASN 378 B ASN 378 1_555 F NA NA . B NA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? 
metalc ? metalc3 A OD1 ASN 382 B ASN 382 1_555 F NA NA . B NA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? 
metalc ? metalc4 F NA NA . B NA 504 1_555 N O HOH . B HOH 617 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.788 ? 
metalc ? metalc5 F NA NA . B NA 504 1_555 N O HOH . B HOH 626 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.621 ? 
metalc ? metalc6 F NA NA . B NA 504 1_555 N O HOH . B HOH 635 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? 
#
_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 324 n n 
C1 C3 MLI sing 325 n n 
C1 H11 MLI sing 326 n n 
C1 H12 MLI sing 327 n n 
C2 O6 MLI doub 328 n n 
C2 O7 MLI sing 329 n n 
C3 O8 MLI doub 330 n n 
C3 O9 MLI sing 331 n n 
#
_atom_sites.entry_id                     6C1R 
_atom_sites.fract_transf_matrix[1][1]    0.01712 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.004935 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.019009 
_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]    0.012409 
_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 3 EFD B 1 501 1 EFD AVA . 
D 4 MLI B 1 502 2 MLI MLI . 
E 4 MLI B 1 503 3 MLI MLI . 
F 5 NA B 1 504 1 NA NA . 
G 6 PGE B 1 505 1 PGE PGE . 
H 7 OLC B 1 506 1 OLC OLC . 
I 7 OLC B 1 507 2 OLC OLC . 
J 8 OLA B 1 508 1 OLA OLA . 
K 8 OLA B 1 509 2 OLA OLA . 
L 8 OLA B 1 510 3 OLA OLA . 
M 8 OLA B 1 511 4 OLA OLA . 
N 9 HOH B 1 601 46 HOH HOH . 
N 9 HOH B 2 602 43 HOH HOH . 
N 9 HOH B 3 603 5 HOH HOH . 
N 9 HOH B 4 604 28 HOH HOH . 
N 9 HOH B 5 605 27 HOH HOH . 
N 9 HOH B 6 606 10 HOH HOH . 
N 9 HOH B 7 607 45 HOH HOH . 
N 9 HOH B 8 608 3 HOH HOH . 
N 9 HOH B 9 609 19 HOH HOH . 
N 9 HOH B 10 610 25 HOH HOH . 
N 9 HOH B 11 611 35 HOH HOH . 
N 9 HOH B 12 612 36 HOH HOH . 
N 9 HOH B 13 613 14 HOH HOH . 
N 9 HOH B 14 614 1 HOH HOH . 
N 9 HOH B 15 615 13 HOH HOH . 
N 9 HOH B 16 616 4 HOH HOH . 
N 9 HOH B 17 617 38 HOH HOH . 
N 9 HOH B 18 618 2 HOH HOH . 
N 9 HOH B 19 619 16 HOH HOH . 
N 9 HOH B 20 620 37 HOH HOH . 
N 9 HOH B 21 621 6 HOH HOH . 
N 9 HOH B 22 622 31 HOH HOH . 
N 9 HOH B 23 623 32 HOH HOH . 
N 9 HOH B 24 624 26 HOH HOH . 
N 9 HOH B 25 625 9 HOH HOH . 
N 9 HOH B 26 626 18 HOH HOH . 
N 9 HOH B 27 627 44 HOH HOH . 
N 9 HOH B 28 628 12 HOH HOH . 
N 9 HOH B 29 629 30 HOH HOH . 
N 9 HOH B 30 630 21 HOH HOH . 
N 9 HOH B 31 631 20 HOH HOH . 
N 9 HOH B 32 632 29 HOH HOH . 
N 9 HOH B 33 633 11 HOH HOH . 
N 9 HOH B 34 634 23 HOH HOH . 
N 9 HOH B 35 635 24 HOH HOH . 
N 9 HOH B 36 636 34 HOH HOH . 
N 9 HOH B 37 637 7 HOH HOH . 
N 9 HOH B 38 638 39 HOH HOH . 
N 9 HOH B 39 639 40 HOH HOH . 
O 9 HOH L 1 101 8 HOH HOH . 
O 9 HOH L 2 102 15 HOH HOH . 
O 9 HOH L 3 103 33 HOH HOH . 
O 9 HOH L 4 104 17 HOH HOH . 
O 9 HOH L 5 105 22 HOH HOH . 
O 9 HOH L 6 106 41 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 . . . D 4 -0.569 4.338 -62.559 1 81.93 ? C1 MLI 502 B 1 
HETATM 2 C C2 MLI . . . D 4 -1.273 5.64 -62.893 1 82.54 ? C2 MLI 502 B 1 
HETATM 3 C C3 MLI . . . D 4 0.683 4.473 -61.711 1 79.62 ? C3 MLI 502 B 1 
HETATM 4 O O6 MLI . . . D 4 -1.122 6.107 -64.041 1 86.16 ? O6 MLI 502 B 1 
HETATM 5 O O7 MLI . . . D 4 -1.994 6.199 -62.039 1 80.24 ? O7 MLI 502 B 1 
HETATM 6 O O8 MLI . . . D 4 1.203 5.599 -61.542 1 79.91 ? O8 MLI 502 B 1 
HETATM 7 O O9 MLI . . . D 4 1.173 3.434 -61.21 1 77.94 ? O9 MLI 502 B 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           20 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           272 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           7 
#