data_7KDP
#
_model_server_result.job_id            te9xqVl0jYi-qBaB0SjvZQ 
_model_server_result.datetime_utc      '2025-02-20 21:44:20' 
_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          7kdp 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":1005}' 
#
_entry.id    7KDP 
#
_exptl.entry_id    7KDP 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          2 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            2-acetamido-2-deoxy-beta-D-glucopyranose 
_entity.pdbx_number_of_molecules    30 
_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            7KDP 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7KDP 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_pdbx_struct_assembly.details               author_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,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA 
_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    ? 
_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
? 2 D N N 
? 2 E N N 
? 2 F N N 
? 2 G N N 
? 2 H N N 
? 2 I N N 
? 2 J N N 
? 2 K N N 
? 2 L N N 
? 2 M N N 
? 2 Q N N 
? 2 R N N 
? 2 S N N 
? 2 T N N 
? 2 U N N 
? 2 V N N 
? 2 W N N 
? 2 X N N 
? 2 Y N N 
? 2 Z N N 
? 2 BA N N 
? 2 CA N N 
? 2 DA N N 
? 2 EA N N 
? 2 FA N N 
? 2 GA N N 
? 2 HA N N 
? 2 IA N N 
? 2 JA N N 
? 2 KA 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 94 A CYS 94 1_555 A SG CYS 551 A CYS 551 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf2 A SG CYS 111 A CYS 111 1_555 A SG CYS 507 A CYS 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf3 A SG CYS 185 A CYS 185 1_555 A SG CYS 250 A CYS 250 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf4 A SG CYS 344 A CYS 344 1_555 A SG CYS 391 A CYS 391 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf5 A SG CYS 574 A CYS 574 1_555 A SG CYS 611 A CYS 611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf6 B SG CYS 94 B CYS 94 1_555 B SG CYS 551 B CYS 551 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf7 B SG CYS 111 B CYS 111 1_555 B SG CYS 507 B CYS 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf8 B SG CYS 185 B CYS 185 1_555 B SG CYS 250 B CYS 250 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf9 B SG CYS 344 B CYS 344 1_555 B SG CYS 391 B CYS 391 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf10 B SG CYS 574 B CYS 574 1_555 B SG CYS 611 B CYS 611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf11 C SG CYS 94 C CYS 94 1_555 C SG CYS 551 C CYS 551 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf12 C SG CYS 111 C CYS 111 1_555 C SG CYS 507 C CYS 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf13 C SG CYS 185 C CYS 185 1_555 C SG CYS 250 C CYS 250 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf14 C SG CYS 344 C CYS 344 1_555 C SG CYS 391 C CYS 391 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf15 C SG CYS 574 C CYS 574 1_555 C SG CYS 611 C CYS 611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
covale ? covale1 A ND2 ASN 208 A ASN 208 1_555 D C1 NAG . A NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? 
covale ? covale2 A ND2 ASN 281 A ASN 281 1_555 E C1 NAG . A NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
covale ? covale3 A ND2 ASN 286 A ASN 286 1_555 F C1 NAG . A NAG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? 
covale ? covale4 A ND2 ASN 302 A ASN 302 1_555 G C1 NAG . A NAG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? 
covale ? covale5 A ND2 ASN 341 A ASN 341 1_555 H C1 NAG . A NAG 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? 
covale ? covale6 A ND2 ASN 383 A ASN 383 1_555 I C1 NAG . A NAG 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
covale ? covale7 A ND2 ASN 405 A ASN 405 1_555 J C1 NAG . A NAG 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? 
covale ? covale8 A ND2 ASN 417 A ASN 417 1_555 K C1 NAG . A NAG 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
covale ? covale9 A ND2 ASN 555 A ASN 555 1_555 L C1 NAG . A NAG 1009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
covale ? covale10 A ND2 ASN 586 A ASN 586 1_555 M C1 NAG . A NAG 1010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? 
covale ? covale11 B ND2 ASN 208 B ASN 208 1_555 Q C1 NAG . B NAG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? 
covale ? covale12 B ND2 ASN 281 B ASN 281 1_555 R C1 NAG . B NAG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
covale ? covale13 B ND2 ASN 286 B ASN 286 1_555 S C1 NAG . B NAG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? 
covale ? covale14 B ND2 ASN 302 B ASN 302 1_555 T C1 NAG . B NAG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? 
covale ? covale15 B ND2 ASN 341 B ASN 341 1_555 U C1 NAG . B NAG 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? 
covale ? covale16 B ND2 ASN 383 B ASN 383 1_555 V C1 NAG . B NAG 1107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
covale ? covale17 B ND2 ASN 405 B ASN 405 1_555 W C1 NAG . B NAG 1108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? 
covale ? covale18 B ND2 ASN 417 B ASN 417 1_555 X C1 NAG . B NAG 1109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
covale ? covale19 B ND2 ASN 555 B ASN 555 1_555 Y C1 NAG . B NAG 1110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
covale ? covale20 B ND2 ASN 586 B ASN 586 1_555 Z C1 NAG . B NAG 1111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
covale ? covale21 C ND2 ASN 208 C ASN 208 1_555 BA C1 NAG . C NAG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? 
covale ? covale22 C ND2 ASN 281 C ASN 281 1_555 CA C1 NAG . C NAG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
covale ? covale23 C ND2 ASN 286 C ASN 286 1_555 DA C1 NAG . C NAG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? 
covale ? covale24 C ND2 ASN 302 C ASN 302 1_555 EA C1 NAG . C NAG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? 
covale ? covale25 C ND2 ASN 341 C ASN 341 1_555 FA C1 NAG . C NAG 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? 
covale ? covale26 C ND2 ASN 383 C ASN 383 1_555 GA C1 NAG . C NAG 1107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
covale ? covale27 C ND2 ASN 405 C ASN 405 1_555 HA C1 NAG . C NAG 1108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? 
covale ? covale28 C ND2 ASN 417 C ASN 417 1_555 IA C1 NAG . C NAG 1109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
covale ? covale29 C ND2 ASN 555 C ASN 555 1_555 JA C1 NAG . C NAG 1110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? 
covale ? covale30 C ND2 ASN 586 C ASN 586 1_555 KA C1 NAG . C NAG 1111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? 
#
_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 235 n n 
C1 O1 NAG sing 236 n n 
C1 O5 NAG sing 237 n n 
C1 H1 NAG sing 238 n n 
C2 C3 NAG sing 239 n n 
C2 N2 NAG sing 240 n n 
C2 H2 NAG sing 241 n n 
C3 C4 NAG sing 242 n n 
C3 O3 NAG sing 243 n n 
C3 H3 NAG sing 244 n n 
C4 C5 NAG sing 245 n n 
C4 O4 NAG sing 246 n n 
C4 H4 NAG sing 247 n n 
C5 C6 NAG sing 248 n n 
C5 O5 NAG sing 249 n n 
C5 H5 NAG sing 250 n n 
C6 O6 NAG sing 251 n n 
C6 H61 NAG sing 252 n n 
C6 H62 NAG sing 253 n n 
C7 C8 NAG sing 254 n n 
C7 N2 NAG sing 255 n n 
C7 O7 NAG doub 256 n n 
C8 H81 NAG sing 257 n n 
C8 H82 NAG sing 258 n n 
C8 H83 NAG sing 259 n n 
N2 HN2 NAG sing 260 n n 
O1 HO1 NAG sing 261 n n 
O3 HO3 NAG sing 262 n n 
O4 HO4 NAG sing 263 n n 
O6 HO6 NAG sing 264 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                     7KDP 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
D 2 NAG A 1 1001 1102 NAG NAG . 
E 2 NAG A 1 1002 1103 NAG NAG . 
F 2 NAG A 1 1003 1104 NAG NAG . 
G 2 NAG A 1 1004 1105 NAG NAG . 
H 2 NAG A 1 1005 1106 NAG NAG . 
I 2 NAG A 1 1006 1107 NAG NAG . 
J 2 NAG A 1 1007 1108 NAG NAG . 
K 2 NAG A 1 1008 1109 NAG NAG . 
L 2 NAG A 1 1009 1110 NAG NAG . 
M 2 NAG A 1 1010 1111 NAG NAG . 
N 3 WCY A 1 1011 1101 WCY PFE . 
O 4 CA A 1 1012 1 CA CA . 
P 3 WCY B 1 1101 1101 WCY PFE . 
Q 2 NAG B 1 1102 1102 NAG NAG . 
R 2 NAG B 1 1103 1103 NAG NAG . 
S 2 NAG B 1 1104 1104 NAG NAG . 
T 2 NAG B 1 1105 1105 NAG NAG . 
U 2 NAG B 1 1106 1106 NAG NAG . 
V 2 NAG B 1 1107 1107 NAG NAG . 
W 2 NAG B 1 1108 1108 NAG NAG . 
X 2 NAG B 1 1109 1109 NAG NAG . 
Y 2 NAG B 1 1110 1110 NAG NAG . 
Z 2 NAG B 1 1111 1111 NAG NAG . 
AA 3 WCY C 1 1101 1101 WCY PFE . 
BA 2 NAG C 1 1102 1102 NAG NAG . 
CA 2 NAG C 1 1103 1103 NAG NAG . 
DA 2 NAG C 1 1104 1104 NAG NAG . 
EA 2 NAG C 1 1105 1105 NAG NAG . 
FA 2 NAG C 1 1106 1106 NAG NAG . 
GA 2 NAG C 1 1107 1107 NAG NAG . 
HA 2 NAG C 1 1108 1108 NAG NAG . 
IA 2 NAG C 1 1109 1109 NAG NAG . 
JA 2 NAG C 1 1110 1110 NAG NAG . 
KA 2 NAG C 1 1111 1111 NAG NAG . 
#
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 . . . H 2 221.215 155.474 186.042 1 143.68 ? C1 NAG 1005 A 1 
HETATM 2 C C2 NAG . . . H 2 220.155 154.688 185.266 1 143.68 ? C2 NAG 1005 A 1 
HETATM 3 C C3 NAG . . . H 2 220.626 153.257 185.023 1 143.68 ? C3 NAG 1005 A 1 
HETATM 4 C C4 NAG . . . H 2 221.998 153.251 184.364 1 143.68 ? C4 NAG 1005 A 1 
HETATM 5 C C5 NAG . . . H 2 222.979 154.091 185.175 1 143.68 ? C5 NAG 1005 A 1 
HETATM 6 C C6 NAG . . . H 2 224.326 154.234 184.506 1 143.68 ? C6 NAG 1005 A 1 
HETATM 7 C C7 NAG . . . H 2 217.759 155.201 185.444 1 143.68 ? C7 NAG 1005 A 1 
HETATM 8 C C8 NAG . . . H 2 216.536 155.118 186.308 1 143.68 ? C8 NAG 1005 A 1 
HETATM 9 N N2 NAG . . . H 2 218.881 154.693 185.966 1 143.68 ? N2 NAG 1005 A 1 
HETATM 10 O O3 NAG . . . H 2 219.686 152.588 184.19 1 143.68 ? O3 NAG 1005 A 1 
HETATM 11 O O4 NAG . . . H 2 222.485 151.917 184.273 1 143.68 ? O4 NAG 1005 A 1 
HETATM 12 O O5 NAG . . . H 2 222.461 155.419 185.344 1 143.68 ? O5 NAG 1005 A 1 
HETATM 13 O O6 NAG . . . H 2 224.219 154.915 183.264 1 143.68 ? O6 NAG 1005 A 1 
HETATM 14 O O7 NAG . . . H 2 217.733 155.705 184.326 1 143.68 ? O7 NAG 1005 A 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    16 
_model_server_stats.query_time_ms           275 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           14 
#