data_6LKN
#
_model_server_result.job_id            '_rX98jMXxwk9hO0XM-opJw' 
_model_server_result.datetime_utc      '2024-11-04 22:37:28' 
_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          6lkn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"W","auth_seq_id":404}' 
#
_entry.id    6LKN 
#
_exptl.entry_id    6LKN 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          5 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            2-acetamido-2-deoxy-beta-D-glucopyranose 
_entity.pdbx_number_of_molecules    16 
_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            6LKN 
_cell.length_a            100.46 
_cell.length_b            232.83 
_cell.length_c            492.89 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6LKN 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    'P 2ac 2ab' 
_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 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 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,I,J,K,L,M,N,O,P,NA 1 1 
C,D,Q,R,S,T,U,V,W,X,OA 2 1 
E,F,Y,Z,AA,BA,CA,DA,EA,FA,PA 3 1 
G,H,GA,HA,IA,JA,KA,LA,MA,QA 4 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 L N N 
? 5 M N N 
? 5 O N N 
? 5 P N N 
? 5 T N N 
? 5 U N N 
? 5 W N N 
? 5 X N N 
? 5 BA N N 
? 5 CA N N 
? 5 EA N N 
? 5 FA N N 
? 5 IA N N 
? 5 JA N N 
? 5 LA N N 
? 5 MA 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 B SG CYS 91 C CYS 91 1_555 B SG CYS 104 C CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf2 B SG CYS 94 C CYS 94 1_555 B SG CYS 102 C CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf3 C SG CYS 165 E CYS 165 1_555 C SG CYS 197 E CYS 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.787 ? 
disulf ? disulf4 D SG CYS 94 F CYS 94 1_555 D SG CYS 102 F CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf5 F SG CYS 91 J CYS 91 1_555 F SG CYS 104 J CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf6 F SG CYS 94 J CYS 94 1_555 F SG CYS 102 J CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf7 H SG CYS 91 N CYS 91 1_555 H SG CYS 104 N CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? 
disulf ? disulf8 H SG CYS 94 N CYS 94 1_555 H SG CYS 102 N CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
covale ? covale1 A C THR 408 A THR 408 1_555 A N BFD 409 A BFD 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale2 A C BFD 409 A BFD 409 1_555 A N LYS 410 A LYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? 
covale ? covale3 C C THR 408 E THR 408 1_555 C N BFD 409 E BFD 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? 
covale ? covale4 C C BFD 409 E BFD 409 1_555 C N LYS 410 E LYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale5 E C THR 408 I THR 408 1_555 E N BFD 409 I BFD 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale6 E C BFD 409 I BFD 409 1_555 E N LYS 410 I LYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale7 G C THR 408 M THR 408 1_555 G N BFD 409 M BFD 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? 
covale ? covale8 G C BFD 409 M BFD 409 1_555 G N LYS 410 M LYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
metalc ? metalc1 A OD2 BFD 409 A BFD 409 1_555 J MG MG . A MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.685 ? 
metalc ? metalc2 A OD1 ASP 816 A ASP 816 1_555 J MG MG . A MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.981 ? 
metalc ? metalc3 A OD1 ASP 820 A ASP 820 1_555 J MG MG . A MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.943 ? 
metalc ? metalc4 J MG MG . A MG 1202 1_555 NA O HOH . A HOH 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? 
metalc ? metalc5 J MG MG . A MG 1202 1_555 NA O HOH . A HOH 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? 
metalc ? metalc6 S MG MG . E MG 1203 1_555 OA O HOH . E HOH 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? 
metalc ? metalc7 S MG MG . E MG 1203 1_555 OA O HOH . E HOH 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? 
metalc ? metalc8 E O THR 411 I THR 411 1_555 AA MG MG . I MG 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.753 ? 
metalc ? metalc9 E OD1 ASP 816 I ASP 816 1_555 AA MG MG . I MG 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.865 ? 
metalc ? metalc10 AA MG MG . I MG 1203 1_555 PA O HOH . I HOH 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? 
metalc ? metalc11 AA MG MG . I MG 1203 1_555 PA O HOH . I HOH 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? 
metalc ? metalc12 G OG1 THR 413 M THR 413 1_555 HA MG MG . M MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.989 ? 
metalc ? metalc13 G OD2 ASP 816 M ASP 816 1_555 HA MG MG . M MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.809 ? 
metalc ? metalc14 HA MG MG . M MG 1202 1_555 QA O HOH . M HOH 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? 
metalc ? metalc15 HA MG MG . M MG 1202 1_555 QA O HOH . M HOH 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? 
#
_chem_comp.formula           'C8 H15 N O6' 
_chem_comp.formula_weight    221.208 
_chem_comp.id                NAG 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-acetamido-2-deoxy-beta-D-glucopyranose 
_chem_comp.type              'd-saccharide, beta linking' 
_chem_comp.pdbx_synonyms     N-acetyl-beta-D-glucosamine;2-acetamido-2-deoxy-beta-D-glucose;2-acetamido-2-deoxy-D-glucose;2-acetamido-2-deoxy-glucose;N-ACETYL-D-GLUCOSAMINE 
#
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 NAG sing 278 n n 
C1 O1 NAG sing 279 n n 
C1 O5 NAG sing 280 n n 
C1 H1 NAG sing 281 n n 
C2 C3 NAG sing 282 n n 
C2 N2 NAG sing 283 n n 
C2 H2 NAG sing 284 n n 
C3 C4 NAG sing 285 n n 
C3 O3 NAG sing 286 n n 
C3 H3 NAG sing 287 n n 
C4 C5 NAG sing 288 n n 
C4 O4 NAG sing 289 n n 
C4 H4 NAG sing 290 n n 
C5 C6 NAG sing 291 n n 
C5 O5 NAG sing 292 n n 
C5 H5 NAG sing 293 n n 
C6 O6 NAG sing 294 n n 
C6 H61 NAG sing 295 n n 
C6 H62 NAG sing 296 n n 
C7 C8 NAG sing 297 n n 
C7 N2 NAG sing 298 n n 
C7 O7 NAG doub 299 n n 
C8 H81 NAG sing 300 n n 
C8 H82 NAG sing 301 n n 
C8 H83 NAG sing 302 n n 
N2 HN2 NAG sing 303 n n 
O1 HO1 NAG sing 304 n n 
O3 HO3 NAG sing 305 n n 
O4 HO4 NAG sing 306 n n 
O6 HO6 NAG sing 307 n n 
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.identifier
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
NAG DGlcpNAcb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 
NAG N-acetyl-b-D-glucopyranosamine 'COMMON NAME' GMML 1 
NAG b-D-GlcpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 
NAG GlcNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 
#
_atom_sites.entry_id                     6LKN 
_atom_sites.fract_transf_matrix[1][1]    0.009954 
_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]    0.004295 
_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]    0.002029 
_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 3 P5S A 1 1201 2000 P5S P5S . 
J 4 MG A 1 1202 2002 MG MO6 . 
K 3 P5S C 1 401 1999 P5S P5S . 
L 5 NAG C 1 402 401 NAG NAG . 
M 5 NAG C 1 403 402 NAG NAG . 
N 6 AH2 C 1 404 403 AH2 MAN . 
O 5 NAG C 1 405 404 NAG NAG . 
P 5 NAG C 1 406 405 NAG NAG . 
Q 3 P5S E 1 1201 1999 P5S P5S . 
R 3 P5S E 1 1202 2000 P5S P5S . 
S 4 MG E 1 1203 2002 MG MO6 . 
T 5 NAG F 1 401 401 NAG NAG . 
U 5 NAG F 1 402 402 NAG NAG . 
V 6 AH2 F 1 403 403 AH2 MAN . 
W 5 NAG F 1 404 404 NAG NAG . 
X 5 NAG F 1 405 405 NAG NAG . 
Y 3 P5S I 1 1201 1999 P5S P5S . 
Z 3 P5S I 1 1202 2000 P5S P5S . 
AA 4 MG I 1 1203 2002 MG MO6 . 
BA 5 NAG J 1 401 401 NAG NAG . 
CA 5 NAG J 1 402 402 NAG NAG . 
DA 6 AH2 J 1 403 403 AH2 MAN . 
EA 5 NAG J 1 404 404 NAG NAG . 
FA 5 NAG J 1 405 405 NAG NAG . 
GA 3 P5S M 1 1201 1999 P5S P5S . 
HA 4 MG M 1 1202 2002 MG MO6 . 
IA 5 NAG N 1 401 401 NAG NAG . 
JA 5 NAG N 1 402 402 NAG NAG . 
KA 6 AH2 N 1 403 403 AH2 MAN . 
LA 5 NAG N 1 404 404 NAG NAG . 
MA 5 NAG N 1 405 405 NAG NAG . 
NA 7 HOH A 1 1301 2002 HOH MO6 . 
NA 7 HOH A 2 1302 2002 HOH MO6 . 
OA 7 HOH E 1 1301 2002 HOH MO6 . 
OA 7 HOH E 2 1302 2002 HOH MO6 . 
PA 7 HOH I 1 1301 2002 HOH MO6 . 
PA 7 HOH I 2 1302 2002 HOH MO6 . 
QA 7 HOH M 1 1301 2002 HOH MO6 . 
QA 7 HOH M 2 1302 2002 HOH MO6 . 
#
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 NAG . . . W 5 -19.625 62.235 -0.365 1 104.73 ? C1 NAG 404 F 1 
HETATM 2 C C2 NAG . . . W 5 -20.327 63.585 -0.214 1 104.73 ? C2 NAG 404 F 1 
HETATM 3 C C3 NAG . . . W 5 -21.427 63.502 0.844 1 96.72 ? C3 NAG 404 F 1 
HETATM 4 C C4 NAG . . . W 5 -22.344 62.323 0.561 1 87.2 ? C4 NAG 404 F 1 
HETATM 5 C C5 NAG . . . W 5 -21.541 61.029 0.498 1 95.89 ? C5 NAG 404 F 1 
HETATM 6 C C6 NAG . . . W 5 -21.728 60.275 -0.796 1 79.67 ? C6 NAG 404 F 1 
HETATM 7 C C7 NAG . . . W 5 -19.625 65.932 -0.017 1 136.64 ? C7 NAG 404 F 1 
HETATM 8 C C8 NAG . . . W 5 -18.52 66.861 0.382 1 139.08 ? C8 NAG 404 F 1 
HETATM 9 N N2 NAG . . . W 5 -19.371 64.627 0.124 1 120.91 ? N2 NAG 404 F 1 
HETATM 10 O O3 NAG . . . W 5 -22.18 64.71 0.846 1 100.05 ? O3 NAG 404 F 1 
HETATM 11 O O4 NAG . . . W 5 -23.316 62.223 1.595 1 86.96 ? O4 NAG 404 F 1 
HETATM 12 O O5 NAG . . . W 5 -20.138 61.309 0.607 1 102.73 ? O5 NAG 404 F 1 
HETATM 13 O O6 NAG . . . W 5 -20.757 59.248 -0.944 1 61.56 ? O6 NAG 404 F 1 
HETATM 14 O O7 NAG . . . W 5 -20.7 66.344 -0.44 1 145.04 ? O7 NAG 404 F 1 
#
_model_server_stats.io_time_ms              100 
_model_server_stats.parse_time_ms           21 
_model_server_stats.create_model_time_ms    77 
_model_server_stats.query_time_ms           277 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           14 
#