data_7LKP
#
_model_server_result.job_id            '_E09dvQVJhwNbknOtEfCvg' 
_model_server_result.datetime_utc      '2024-11-08 19:22:03' 
_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          7lkp 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":2303}' 
#
_entry.id    7LKP 
#
_exptl.entry_id    7LKP 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-acetamido-2-deoxy-beta-D-glucopyranose 
_entity.pdbx_number_of_molecules    6 
_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            7LKP 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7LKP 
_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    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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
? 4 D N N 
? 4 E N N 
? 4 F N N 
? 4 G N N 
? 4 H N N 
? 4 I N N 
#
loop_
_pdbx_entity_branch.entity_id
_pdbx_entity_branch.type
2 oligosaccharide 
3 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 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 
3 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 
4 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 
5 ? 3 4 3 BMA BMA C1 O1 . O3 HO3 . sing 
6 ? 3 5 3 BMA BMA C1 O1 . O6 HO6 . 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 B NAG 1 B 1 NAG B 2 NAG 
2 n B NAG 2 B 2 NAG B 3 NAG 
2 n B BMA 3 B 3 BMA B 4 BMA 
3 n C NAG 1 C 1 NAG B 8 NAG 
3 n C NAG 2 C 2 NAG B 9 NAG 
3 n C BMA 3 C 3 BMA B 10 BMA 
3 n C BMA 4 C 4 BMA B 11 BMA 
3 n C BMA 5 C 5 BMA B 12 BMA 
#
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 54 A CYS 54 1_555 A SG CYS 81 A CYS 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf2 A SG CYS 75 A CYS 75 1_555 A SG CYS 324 A CYS 324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf3 A SG CYS 370 A CYS 370 1_555 A SG CYS 519 A CYS 519 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
disulf ? disulf4 A SG CYS 641 A CYS 641 1_555 A SG CYS 1490 A CYS 1490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf5 A SG CYS 1444 A CYS 1444 1_555 A SG CYS 1455 A CYS 1455 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf6 A SG CYS 1488 A CYS 1488 1_555 A SG CYS 1502 A CYS 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
covale ? covale1 A ND2 ASN 98 A ASN 98 1_555 I C1 NAG . A NAG 2306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? 
covale ? covale2 A ND2 ASN 415 A ASN 415 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
covale ? covale3 A ND2 ASN 444 A ASN 444 1_555 D C1 NAG . A NAG 2301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
covale ? covale4 A ND2 ASN 504 A ASN 504 1_555 E C1 NAG . A NAG 2302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? 
covale ? covale5 A ND2 ASN 1469 A ASN 1469 1_555 F C1 NAG . A NAG 2303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
covale ? covale6 A ND2 ASN 1529 A ASN 1529 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.421 ? 
covale ? covale7 A ND2 ASN 1588 A ASN 1588 1_555 G C1 NAG . A NAG 2304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
covale ? covale8 A ND2 ASN 1662 A ASN 1662 1_555 H C1 NAG . A NAG 2305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? 
covale ? covale9 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? 
covale ? covale10 B O4 NAG . B NAG 2 1_555 B C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? 
covale ? covale11 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
covale ? covale12 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? 
covale ? covale13 C O3 BMA . C BMA 3 1_555 C C1 BMA . C BMA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? 
covale ? covale14 C O6 BMA . C BMA 3 1_555 C C1 BMA . C BMA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? 
#
_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 523 n n 
C1 O1 NAG sing 524 n n 
C1 O5 NAG sing 525 n n 
C1 H1 NAG sing 526 n n 
C2 C3 NAG sing 527 n n 
C2 N2 NAG sing 528 n n 
C2 H2 NAG sing 529 n n 
C3 C4 NAG sing 530 n n 
C3 O3 NAG sing 531 n n 
C3 H3 NAG sing 532 n n 
C4 C5 NAG sing 533 n n 
C4 O4 NAG sing 534 n n 
C4 H4 NAG sing 535 n n 
C5 C6 NAG sing 536 n n 
C5 O5 NAG sing 537 n n 
C5 H5 NAG sing 538 n n 
C6 O6 NAG sing 539 n n 
C6 H61 NAG sing 540 n n 
C6 H62 NAG sing 541 n n 
C7 C8 NAG sing 542 n n 
C7 N2 NAG sing 543 n n 
C7 O7 NAG doub 544 n n 
C8 H81 NAG sing 545 n n 
C8 H82 NAG sing 546 n n 
C8 H83 NAG sing 547 n n 
N2 HN2 NAG sing 548 n n 
O1 HO1 NAG sing 549 n n 
O3 HO3 NAG sing 550 n n 
O4 HO4 NAG sing 551 n n 
O6 HO6 NAG sing 552 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                     7LKP 
_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 4 NAG A 1 2301 5 NAG NAG . 
E 4 NAG A 1 2302 6 NAG NAG . 
F 4 NAG A 1 2303 7 NAG NAG . 
G 4 NAG A 1 2304 13 NAG NAG . 
H 4 NAG A 1 2305 14 NAG NAG . 
I 4 NAG A 1 2306 15 NAG NAG . 
J 5 CLR A 1 2307 1 CLR CLR . 
K 6 POV A 1 2308 2 POV POV . 
L 5 CLR A 1 2309 3 CLR CLR . 
M 7 AJP A 1 2310 4 AJP AJP . 
N 5 CLR A 1 2311 5 CLR CLR . 
O 5 CLR A 1 2312 6 CLR CLR . 
P 5 CLR A 1 2313 7 CLR CLR . 
Q 5 CLR A 1 2314 8 CLR CLR . 
R 5 CLR A 1 2315 9 CLR CLR . 
S 6 POV A 1 2316 10 POV POV . 
T 6 POV A 1 2317 11 POV POV . 
U 6 POV A 1 2318 12 POV POV . 
V 6 POV A 1 2319 13 POV POV . 
W 6 POV A 1 2320 14 POV POV . 
X 6 POV A 1 2321 15 POV POV . 
#
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 . . . F 4 188.331 225.251 213.806 1 158.03 ? C1 NAG 2303 A 1 
HETATM 2 C C2 NAG . . . F 4 188.216 226.732 214.173 1 158.03 ? C2 NAG 2303 A 1 
HETATM 3 C C3 NAG . . . F 4 189.013 227.599 213.193 1 158.03 ? C3 NAG 2303 A 1 
HETATM 4 C C4 NAG . . . F 4 188.727 227.222 211.743 1 158.03 ? C4 NAG 2303 A 1 
HETATM 5 C C5 NAG . . . F 4 188.803 225.712 211.54 1 158.03 ? C5 NAG 2303 A 1 
HETATM 6 C C6 NAG . . . F 4 189.766 225.307 210.449 1 158.03 ? C6 NAG 2303 A 1 
HETATM 7 C C7 NAG . . . F 4 186.267 227.766 215.255 1 158.03 ? C7 NAG 2303 A 1 
HETATM 8 C C8 NAG . . . F 4 187.169 228.017 216.426 1 158.03 ? C8 NAG 2303 A 1 
HETATM 9 N N2 NAG . . . F 4 186.823 227.149 214.208 1 158.03 ? N2 NAG 2303 A 1 
HETATM 10 O O3 NAG . . . F 4 190.403 227.462 213.464 1 158.03 ? O3 NAG 2303 A 1 
HETATM 11 O O4 NAG . . . F 4 187.432 227.678 211.37 1 158.03 ? O4 NAG 2303 A 1 
HETATM 12 O O5 NAG . . . F 4 189.26 225.091 212.746 1 158.03 ? O5 NAG 2303 A 1 
HETATM 13 O O6 NAG . . . F 4 189.648 223.925 210.139 1 158.03 ? O6 NAG 2303 A 1 
HETATM 14 O O7 NAG . . . F 4 185.088 228.107 215.257 1 158.03 ? O7 NAG 2303 A 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    16 
_model_server_stats.query_time_ms           274 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           14 
#