data_4YTN
#
_model_server_result.job_id            PjLPLv1FyHuCfqfaFZHT0w 
_model_server_result.datetime_utc      '2024-11-24 19:43:45' 
_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          4ytn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"P","auth_seq_id":701}' 
#
_entry.id    4YTN 
#
_exptl.entry_id    4YTN 
_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    2 
_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            4YTN 
_cell.length_a            123.614 
_cell.length_b            125.483 
_cell.length_c            219.67 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4YTN 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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 tetrameric 4 author_and_software_defined_assembly 1 
PISA tetrameric 4 author_and_software_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,D,I,J,K,L,M,N,O,W,X,Y,Z 1 1 
E,F,G,H,P,Q,R,S,T,U,V,AA,BA 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 P 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 191 A CYS 191 1_555 A SG CYS 193 A CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? 
disulf ? disulf2 E SG CYS 191 E CYS 191 1_555 E SG CYS 193 E CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
metalc ? metalc1 B SG CYS 89 B CYS 89 1_555 K FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? 
metalc ? metalc2 B SG CYS 94 B CYS 94 1_555 K FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? 
metalc ? metalc3 B SG CYS 97 B CYS 97 1_555 K FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? 
metalc ? metalc4 B SG CYS 109 B CYS 109 1_555 K FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? 
metalc ? metalc5 B SG CYS 182 B CYS 182 1_555 L FE3 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? 
metalc ? metalc6 B SG CYS 185 B CYS 185 1_555 L FE1 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? 
metalc ? metalc7 B SG CYS 188 B CYS 188 1_555 L FE2 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? 
metalc ? metalc8 B SG CYS 192 B CYS 192 1_555 M FE4 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? 
metalc ? metalc9 B SG CYS 239 B CYS 239 1_555 M FE1 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? 
metalc ? metalc10 B SG CYS 245 B CYS 245 1_555 M FE3 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? 
metalc ? metalc11 B SG CYS 249 B CYS 249 1_555 L FE4 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? 
metalc ? metalc12 C NE2 HIS 131 C HIS 131 1_555 N FE HEM . C HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? 
metalc ? metalc13 N FE HEM . C HEM 201 1_555 D NE2 HIS 95 D HIS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? 
metalc ? metalc14 F SG CYS 89 F CYS 89 1_555 R FE2 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? 
metalc ? metalc15 F SG CYS 94 F CYS 94 1_555 R FE2 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? 
metalc ? metalc16 F SG CYS 97 F CYS 97 1_555 R FE1 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? 
metalc ? metalc17 F SG CYS 109 F CYS 109 1_555 R FE1 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? 
metalc ? metalc18 F SG CYS 182 F CYS 182 1_555 S FE3 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? 
metalc ? metalc19 F SG CYS 185 F CYS 185 1_555 S FE1 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? 
metalc ? metalc20 F SG CYS 188 F CYS 188 1_555 S FE2 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? 
metalc ? metalc21 F SG CYS 192 F CYS 192 1_555 T FE4 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? 
metalc ? metalc22 F SG CYS 239 F CYS 239 1_555 T FE1 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? 
metalc ? metalc23 F SG CYS 245 F CYS 245 1_555 T FE3 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? 
metalc ? metalc24 F SG CYS 249 F CYS 249 1_555 S FE4 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? 
metalc ? metalc25 G NE2 HIS 131 G HIS 131 1_555 V FE HEM . G HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? 
metalc ? metalc26 V FE HEM . G HEM 201 1_555 H NE2 HIS 95 H HIS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? 
#
_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 465 n n 
C1 C3 MLI sing 466 n n 
C1 H11 MLI sing 467 n n 
C1 H12 MLI sing 468 n n 
C2 O6 MLI doub 469 n n 
C2 O7 MLI sing 470 n n 
C3 O8 MLI doub 471 n n 
C3 O9 MLI sing 472 n n 
#
_atom_sites.entry_id                     4YTN 
_atom_sites.fract_transf_matrix[1][1]    0.00809 
_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]    0.007969 
_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]    0.004552 
_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
I 5 MLI A 1 701 701 MLI MLI . 
J 6 FAD A 1 702 702 FAD FAD . 
K 7 FES B 1 301 301 FES FES . 
L 8 SF4 B 1 302 302 SF4 SF4 . 
M 9 F3S B 1 303 303 F3S F3S . 
N 10 HEM C 1 201 201 HEM HEM . 
O 11 FD8 C 1 202 301 FD8 DRG . 
P 5 MLI E 1 701 701 MLI MLI . 
Q 6 FAD E 1 702 702 FAD FAD . 
R 7 FES F 1 301 301 FES FES . 
S 8 SF4 F 1 302 302 SF4 SF4 . 
T 9 F3S F 1 303 303 F3S F3S . 
U 11 FD8 F 1 304 301 FD8 DRG . 
V 10 HEM G 1 201 201 HEM HEM . 
W 12 HOH A 1 801 3 HOH HOH . 
W 12 HOH A 2 802 8 HOH HOH . 
W 12 HOH A 3 803 22 HOH HOH . 
W 12 HOH A 4 804 1 HOH HOH . 
W 12 HOH A 5 805 40 HOH HOH . 
W 12 HOH A 6 806 6 HOH HOH . 
W 12 HOH A 7 807 34 HOH HOH . 
W 12 HOH A 8 808 29 HOH HOH . 
W 12 HOH A 9 809 17 HOH HOH . 
W 12 HOH A 10 810 7 HOH HOH . 
W 12 HOH A 11 811 32 HOH HOH . 
W 12 HOH A 12 812 16 HOH HOH . 
W 12 HOH A 13 813 15 HOH HOH . 
W 12 HOH A 14 814 20 HOH HOH . 
W 12 HOH A 15 815 5 HOH HOH . 
W 12 HOH A 16 816 10 HOH HOH . 
W 12 HOH A 17 817 26 HOH HOH . 
X 12 HOH B 1 401 30 HOH HOH . 
X 12 HOH B 2 402 28 HOH HOH . 
X 12 HOH B 3 403 12 HOH HOH . 
X 12 HOH B 4 404 35 HOH HOH . 
Y 12 HOH C 1 301 13 HOH HOH . 
Y 12 HOH C 2 302 9 HOH HOH . 
Y 12 HOH C 3 303 33 HOH HOH . 
Y 12 HOH C 4 304 37 HOH HOH . 
Z 12 HOH D 1 201 25 HOH HOH . 
Z 12 HOH D 2 202 39 HOH HOH . 
AA 12 HOH E 1 801 2 HOH HOH . 
AA 12 HOH E 2 802 21 HOH HOH . 
AA 12 HOH E 3 803 14 HOH HOH . 
AA 12 HOH E 4 804 31 HOH HOH . 
AA 12 HOH E 5 805 24 HOH HOH . 
AA 12 HOH E 6 806 11 HOH HOH . 
AA 12 HOH E 7 807 38 HOH HOH . 
AA 12 HOH E 8 808 4 HOH HOH . 
AA 12 HOH E 9 809 36 HOH HOH . 
AA 12 HOH E 10 810 23 HOH HOH . 
AA 12 HOH E 11 811 18 HOH HOH . 
AA 12 HOH E 12 812 19 HOH HOH . 
BA 12 HOH H 1 201 27 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 . . . P 5 -40.933 -2.929 -13.026 1 51.77 ? C1 MLI 701 E 1 
HETATM 2 C C2 MLI . . . P 5 -42.07 -2.87 -14.011 1 51.72 ? C2 MLI 701 E 1 
HETATM 3 C C3 MLI . . . P 5 -40.228 -4.249 -13.144 1 52.95 ? C3 MLI 701 E 1 
HETATM 4 O O6 MLI . . . P 5 -42.355 -3.895 -14.667 1 49.01 ? O6 MLI 701 E 1 
HETATM 5 O O7 MLI . . . P 5 -42.712 -1.796 -14.11 1 51.09 ? O7 MLI 701 E 1 
HETATM 6 O O8 MLI . . . P 5 -39.108 -4.264 -13.689 1 56.84 ? O8 MLI 701 E 1 
HETATM 7 O O9 MLI . . . P 5 -40.78 -5.275 -12.695 1 51.32 ? O9 MLI 701 E 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    20 
_model_server_stats.query_time_ms           305 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           7 
#