data_4KGL
#
_model_server_result.job_id            VvQEcOveoIyP60aMeWJr9w 
_model_server_result.datetime_utc      '2024-11-01 07:31:04' 
_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          4kgl 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"P","auth_seq_id":918}' 
#
_entry.id    4KGL 
#
_exptl.entry_id    4KGL 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              177.155 
_entity.id                          7 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(2R,3R,4R,5S)-3,4,5-trihydroxypiperidine-2-carboxylic acid' 
_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         120 
_cell.entry_id            4KGL 
_cell.length_a            259.359 
_cell.length_b            259.359 
_cell.length_c            71.568 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4KGL 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        146 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'H 3' 
#
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 monomeric 1 software_defined_assembly 1 
PISA monomeric 1 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,C,D,G,H,I,Q 1 1 
B,E,F,J,K,L,M,N,O,P,R 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
? 7 I N N 
? 7 P N N 
#
loop_
_pdbx_entity_branch.entity_id
_pdbx_entity_branch.type
2 oligosaccharide 
3 oligosaccharide 
4 oligosaccharide 
#
loop_
_pdbx_entity_branch_link.link_id
_pdbx_entity_branch_link.details
_pdbx_entity_branch_link.entity_id
_pdbx_entity_branch_link.entity_branch_list_num_1
_pdbx_entity_branch_link.entity_branch_list_num_2
_pdbx_entity_branch_link.comp_id_1
_pdbx_entity_branch_link.comp_id_2
_pdbx_entity_branch_link.atom_id_1
_pdbx_entity_branch_link.leaving_atom_id_1
_pdbx_entity_branch_link.atom_stereo_config_1
_pdbx_entity_branch_link.atom_id_2
_pdbx_entity_branch_link.leaving_atom_id_2
_pdbx_entity_branch_link.atom_stereo_config_2
_pdbx_entity_branch_link.value_order
1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 
2 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 
3 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 
4 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . sing 
5 ? 3 5 3 MAN BMA C1 O1 . O6 HO6 . sing 
6 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 
7 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 
8 ? 4 4 3 MAN BMA C1 O1 . O6 HO6 . sing 
9 ? 4 5 4 MAN MAN C1 O1 . O6 HO6 . sing 
10 ? 4 6 5 MAN MAN C1 O1 . O2 HO2 . sing 
11 ? 4 7 4 MAN MAN C1 O1 . O3 HO3 . sing 
12 ? 4 8 3 MAN BMA C1 O1 . O3 HO3 . sing 
13 ? 4 9 8 MAN MAN C1 O1 . O2 HO2 . sing 
#
loop_
_pdbx_branch_scheme.entity_id
_pdbx_branch_scheme.hetero
_pdbx_branch_scheme.asym_id
_pdbx_branch_scheme.mon_id
_pdbx_branch_scheme.num
_pdbx_branch_scheme.pdb_asym_id
_pdbx_branch_scheme.pdb_seq_num
_pdbx_branch_scheme.pdb_mon_id
_pdbx_branch_scheme.auth_asym_id
_pdbx_branch_scheme.auth_seq_num
_pdbx_branch_scheme.auth_mon_id
2 n C NAG 1 C 1 NAG C 951 NAG 
2 n C NAG 2 C 2 NAG C 952 NAG 
3 n D NAG 1 D 1 NAG C 991 NAG 
3 n D NAG 2 D 2 NAG C 992 NAG 
3 n D BMA 3 D 3 BMA C 993 BMA 
3 n D MAN 4 D 4 MAN C 995 MAN 
3 n D MAN 5 D 5 MAN C 994 MAN 
2 n E NAG 1 E 1 NAG D 951 NAG 
2 n E NAG 2 E 2 NAG D 952 NAG 
4 n F NAG 1 F 1 NAG D 991 NAG 
4 n F NAG 2 F 2 NAG D 992 NAG 
4 n F BMA 3 F 3 BMA D 993 BMA 
4 n F MAN 4 F 4 MAN D 994 MAN 
4 n F MAN 5 F 5 MAN D 997 MAN 
4 n F MAN 6 F 6 MAN D 998 MAN 
4 n F MAN 7 F 7 MAN D 996 MAN 
4 n F MAN 8 F 8 MAN D 995 MAN 
4 n F MAN 9 F 9 MAN D 999 MAN 
#
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 515 A CYS 541 1_555 A SG CYS 551 A CYS 577 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
disulf ? disulf2 B SG CYS 515 B CYS 541 1_555 B SG CYS 551 B CYS 577 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.035 ? 
covale ? covale1 A ND2 ASN 84 A ASN 110 1_555 G C1 NAG . A NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? 
covale ? covale2 A ND2 ASN 346 A ASN 372 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? 
covale ? covale3 A ND2 ASN 389 A ASN 415 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? 
covale ? covale4 B ND2 ASN 84 B ASN 110 1_555 J C1 NAG . B NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? 
covale ? covale5 B ND2 ASN 346 B ASN 372 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? 
covale ? covale6 B ND2 ASN 389 B ASN 415 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? 
covale ? covale7 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? 
covale ? covale8 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? 
covale ? covale9 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
covale ? covale10 D O3 BMA . D BMA 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
covale ? covale11 D O6 BMA . D BMA 3 1_555 D C1 MAN . D MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? 
covale ? covale12 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? 
covale ? covale13 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? 
covale ? covale14 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? 
covale ? covale15 F O6 BMA . F BMA 3 1_555 F C1 MAN . F MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? 
covale ? covale16 F O3 BMA . F BMA 3 1_555 F C1 MAN . F MAN 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? 
covale ? covale17 F O6 MAN . F MAN 4 1_555 F C1 MAN . F MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
covale ? covale18 F O3 MAN . F MAN 4 1_555 F C1 MAN . F MAN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? 
covale ? covale19 F O2 MAN . F MAN 5 1_555 F C1 MAN . F MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
covale ? covale20 F O2 MAN . F MAN 8 1_555 F C1 MAN . F MAN 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
#
_chem_comp.formula           'C6 H11 N O5' 
_chem_comp.formula_weight    177.155 
_chem_comp.id                IDJ 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(2R,3R,4R,5S)-3,4,5-trihydroxypiperidine-2-carboxylic acid' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     '[2R,3R,4R,5S]-2-carboxy-3,4,5-trihydroxy-piperidine' 
#
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 N5 IDJ sing 189 n n 
C1 C2 IDJ sing 190 n n 
N5 C5 IDJ sing 191 n n 
O2 C2 IDJ sing 192 n n 
C2 C3 IDJ sing 193 n n 
C5 C6 IDJ sing 194 n n 
C5 C4 IDJ sing 195 n n 
C6 O6A IDJ doub 196 n n 
C6 O6B IDJ sing 197 n n 
C3 C4 IDJ sing 198 n n 
C3 O3 IDJ sing 199 n n 
C4 O4 IDJ sing 200 n n 
O6B H1 IDJ sing 201 n n 
C5 H2 IDJ sing 202 n n 
N5 H3 IDJ sing 203 n n 
C4 H5 IDJ sing 204 n n 
O4 H6 IDJ sing 205 n n 
C3 H7 IDJ sing 206 n n 
O3 H8 IDJ sing 207 n n 
C2 H9 IDJ sing 208 n n 
O2 H10 IDJ sing 209 n n 
C1 H11 IDJ sing 210 n n 
C1 H12 IDJ sing 211 n n 
#
_atom_sites.entry_id                     4KGL 
_atom_sites.fract_transf_matrix[1][1]    0.003856 
_atom_sites.fract_transf_matrix[1][2]    0.002226 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.004452 
_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]    0.013973 
_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 5 NAG A 1 901 901 NAG NAG . 
H 6 GOL A 1 909 2 GOL GOL . 
I 7 IDJ A 1 910 1 IDJ IDJ . 
J 5 NAG B 1 901 901 NAG NAG . 
K 6 GOL B 1 913 1 GOL GOL . 
L 6 GOL B 1 914 3 GOL GOL . 
M 6 GOL B 1 915 4 GOL GOL . 
N 6 GOL B 1 916 5 GOL GOL . 
O 8 TLA B 1 917 1 TLA TLA . 
P 7 IDJ B 1 918 2 IDJ IDJ . 
Q 9 HOH A 1 1001 4 HOH HOH . 
Q 9 HOH A 2 1002 8 HOH HOH . 
Q 9 HOH A 3 1003 10 HOH HOH . 
Q 9 HOH A 4 1004 12 HOH HOH . 
Q 9 HOH A 5 1005 14 HOH HOH . 
Q 9 HOH A 6 1006 15 HOH HOH . 
Q 9 HOH A 7 1007 18 HOH HOH . 
Q 9 HOH A 8 1008 21 HOH HOH . 
Q 9 HOH A 9 1009 31 HOH HOH . 
Q 9 HOH A 10 1010 33 HOH HOH . 
Q 9 HOH A 11 1011 37 HOH HOH . 
Q 9 HOH A 12 1012 38 HOH HOH . 
Q 9 HOH A 13 1013 39 HOH HOH . 
Q 9 HOH A 14 1014 42 HOH HOH . 
Q 9 HOH A 15 1015 43 HOH HOH . 
Q 9 HOH A 16 1016 44 HOH HOH . 
Q 9 HOH A 17 1017 45 HOH HOH . 
Q 9 HOH A 18 1018 50 HOH HOH . 
Q 9 HOH A 19 1019 51 HOH HOH . 
Q 9 HOH A 20 1020 54 HOH HOH . 
R 9 HOH B 1 1001 46 HOH HOH . 
R 9 HOH B 2 1002 1 HOH HOH . 
R 9 HOH B 3 1003 2 HOH HOH . 
R 9 HOH B 4 1004 3 HOH HOH . 
R 9 HOH B 5 1005 5 HOH HOH . 
R 9 HOH B 6 1006 6 HOH HOH . 
R 9 HOH B 7 1007 7 HOH HOH . 
R 9 HOH B 8 1008 9 HOH HOH . 
R 9 HOH B 9 1009 11 HOH HOH . 
R 9 HOH B 10 1010 13 HOH HOH . 
R 9 HOH B 11 1011 16 HOH HOH . 
R 9 HOH B 12 1012 17 HOH HOH . 
R 9 HOH B 13 1013 19 HOH HOH . 
R 9 HOH B 14 1014 20 HOH HOH . 
R 9 HOH B 15 1015 22 HOH HOH . 
R 9 HOH B 16 1016 23 HOH HOH . 
R 9 HOH B 17 1017 24 HOH HOH . 
R 9 HOH B 18 1018 25 HOH HOH . 
R 9 HOH B 19 1019 26 HOH HOH . 
R 9 HOH B 20 1020 27 HOH HOH . 
R 9 HOH B 21 1021 29 HOH HOH . 
R 9 HOH B 22 1022 30 HOH HOH . 
R 9 HOH B 23 1023 32 HOH HOH . 
R 9 HOH B 24 1024 34 HOH HOH . 
R 9 HOH B 25 1025 35 HOH HOH . 
R 9 HOH B 26 1026 36 HOH HOH . 
R 9 HOH B 27 1027 40 HOH HOH . 
R 9 HOH B 28 1028 41 HOH HOH . 
R 9 HOH B 29 1029 47 HOH HOH . 
R 9 HOH B 30 1030 48 HOH HOH . 
R 9 HOH B 31 1031 49 HOH HOH . 
R 9 HOH B 32 1032 52 HOH HOH . 
R 9 HOH B 33 1033 53 HOH HOH . 
R 9 HOH B 34 1034 55 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 O O6B IDJ . . . P 7 295.844 -24.87 -26.435 1 69.49 ? O6B IDJ 918 B 1 
HETATM 2 C C6 IDJ . . . P 7 294.884 -25.313 -27.106 1 72.13 ? C6 IDJ 918 B 1 
HETATM 3 O O6A IDJ . . . P 7 294.575 -24.856 -28.233 1 69.01 ? O6A IDJ 918 B 1 
HETATM 4 C C5 IDJ . . . P 7 294.078 -26.447 -26.523 1 73.68 ? C5 IDJ 918 B 1 
HETATM 5 N N5 IDJ . . . P 7 293.104 -26.998 -27.457 1 77.74 ? N5 IDJ 918 B 1 
HETATM 6 C C4 IDJ . . . P 7 293.386 -26.048 -25.209 1 73.73 ? C4 IDJ 918 B 1 
HETATM 7 O O4 IDJ . . . P 7 292.809 -24.734 -25.325 1 71.12 ? O4 IDJ 918 B 1 
HETATM 8 C C3 IDJ . . . P 7 292.3 -27.041 -24.746 1 74.89 ? C3 IDJ 918 B 1 
HETATM 9 O O3 IDJ . . . P 7 292.55 -27.425 -23.383 1 75.22 ? O3 IDJ 918 B 1 
HETATM 10 C C2 IDJ . . . P 7 292.115 -28.322 -25.585 1 74 ? C2 IDJ 918 B 1 
HETATM 11 O O2 IDJ . . . P 7 290.782 -28.803 -25.364 1 70.22 ? O2 IDJ 918 B 1 
HETATM 12 C C1 IDJ . . . P 7 292.334 -28.181 -27.099 1 75.24 ? C1 IDJ 918 B 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    19 
_model_server_stats.query_time_ms           320 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           12 
#