data_7XBF
#
_model_server_result.job_id            x99ZSS10HtJlmBpGi80_JA 
_model_server_result.datetime_utc      '2024-11-21 08:47:20' 
_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          7xbf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Q","auth_seq_id":601}' 
#
_entry.id    7XBF 
#
_exptl.entry_id    7XBF 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-acetamido-2-deoxy-beta-D-glucopyranose 
_entity.pdbx_number_of_molecules    11 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          93.261 
_cell.angle_gamma         90 
_cell.entry_id            7XBF 
_cell.length_a            81.391 
_cell.length_b            123.891 
_cell.length_c            112.787 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7XBF 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    'P 2yb' 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? dimeric 2 author_defined_assembly 1 
? dimeric 2 author_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,E,F,G,H,I,J,K 1 1 
C,D,L,M,N,O,P,Q 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
? 3 E N N 
? 3 F N N 
? 3 G N N 
? 3 H N N 
? 3 I N N 
? 3 K N N 
? 3 L N N 
? 3 M N N 
? 3 N N N 
? 3 O N N 
? 3 Q 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 327 A CYS 344 1_555 A SG CYS 344 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf2 A SG CYS 513 A CYS 530 1_555 A SG CYS 525 A CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf3 B SG CYS 38 B CYS 323 1_555 B SG CYS 63 B CYS 348 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf4 B SG CYS 81 B CYS 366 1_555 B SG CYS 134 B CYS 419 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf5 B SG CYS 93 B CYS 378 1_555 B SG CYS 226 B CYS 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf6 B SG CYS 182 B CYS 467 1_555 B SG CYS 189 B CYS 474 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf7 C SG CYS 116 C CYS 133 1_555 C SG CYS 124 C CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf8 C SG CYS 327 C CYS 344 1_555 C SG CYS 344 C CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf9 C SG CYS 513 C CYS 530 1_555 C SG CYS 525 C CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
disulf ? disulf10 D SG CYS 38 D CYS 323 1_555 D SG CYS 63 D CYS 348 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf11 D SG CYS 81 D CYS 366 1_555 D SG CYS 134 D CYS 419 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf12 D SG CYS 93 D CYS 378 1_555 D SG CYS 226 D CYS 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf13 D SG CYS 182 D CYS 467 1_555 D SG CYS 189 D CYS 474 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
covale ? covale1 A ND2 ASN 36 A ASN 53 1_555 H C1 NAG . A NAG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? 
covale ? covale2 A ND2 ASN 73 A ASN 90 1_555 F C1 NAG . A NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
covale ? covale3 A ND2 ASN 86 A ASN 103 1_555 E C1 NAG . A NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? 
covale ? covale4 A ND2 ASN 305 A ASN 322 1_555 I C1 NAG . A NAG 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? 
covale ? covale5 A ND2 ASN 529 A ASN 546 1_555 G C1 NAG . A NAG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? 
covale ? covale6 B ND2 ASN 45 B ASN 330 1_555 K C1 NAG . B NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? 
covale ? covale7 C ND2 ASN 36 C ASN 53 1_555 L C1 NAG . C NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? 
covale ? covale8 C ND2 ASN 73 C ASN 90 1_555 M C1 NAG . C NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? 
covale ? covale9 C ND2 ASN 305 C ASN 322 1_555 N C1 NAG . C NAG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? 
covale ? covale10 C ND2 ASN 529 C ASN 546 1_555 O C1 NAG . C NAG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? 
covale ? covale11 D ND2 ASN 45 D ASN 330 1_555 Q C1 NAG . D NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? 
metalc ? metalc1 A NE2 HIS 357 A HIS 374 1_555 J ZN ZN . A ZN 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? 
metalc ? metalc2 A NE2 HIS 361 A HIS 378 1_555 J ZN ZN . A ZN 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? 
metalc ? metalc3 A OE2 GLU 385 A GLU 402 1_555 J ZN ZN . A ZN 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? 
metalc ? metalc4 C NE2 HIS 357 C HIS 374 1_555 P ZN ZN . C ZN 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? 
metalc ? metalc5 C NE2 HIS 361 C HIS 378 1_555 P ZN ZN . C ZN 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? 
metalc ? metalc6 C OE2 GLU 385 C GLU 402 1_555 P ZN ZN . C ZN 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? 
#
_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                     7XBF 
_atom_sites.fract_transf_matrix[1][1]    0.012286 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.0007 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008072 
_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]    0.008881 
_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
E 3 NAG A 1 701 701 NAG NAG . 
F 3 NAG A 1 702 801 NAG NAG . 
G 3 NAG A 1 703 901 NAG NAG . 
H 3 NAG A 1 704 1001 NAG NAG . 
I 3 NAG A 1 705 1002 NAG NAG . 
J 4 ZN A 1 706 2001 ZN ZN . 
K 3 NAG B 1 601 688 NAG NAG . 
L 3 NAG C 1 701 719 NAG NAG . 
M 3 NAG C 1 702 819 NAG NAG . 
N 3 NAG C 1 703 919 NAG NAG . 
O 3 NAG C 1 704 1020 NAG NAG . 
P 4 ZN C 1 705 2001 ZN ZN . 
Q 3 NAG D 1 601 523 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 . . . Q 3 -8.779 51.764 87.033 1 137.62 ? C1 NAG 601 D 1 
HETATM 2 C C2 NAG . . . Q 3 -10.166 52.19 86.53 1 141.88 ? C2 NAG 601 D 1 
HETATM 3 C C3 NAG . . . Q 3 -10.296 53.715 86.524 1 150.12 ? C3 NAG 601 D 1 
HETATM 4 C C4 NAG . . . Q 3 -9.923 54.296 87.881 1 156.85 ? C4 NAG 601 D 1 
HETATM 5 C C5 NAG . . . Q 3 -8.529 53.825 88.273 1 154.9 ? C5 NAG 601 D 1 
HETATM 6 C C6 NAG . . . Q 3 -8.098 54.307 89.641 1 149.87 ? C6 NAG 601 D 1 
HETATM 7 C C7 NAG . . . Q 3 -11.648 51.458 84.711 1 137.56 ? C7 NAG 601 D 1 
HETATM 8 C C8 NAG . . . Q 3 -11.719 50.907 83.319 1 132.51 ? C8 NAG 601 D 1 
HETATM 9 N N2 NAG . . . Q 3 -10.42 51.654 85.202 1 134.79 ? N2 NAG 601 D 1 
HETATM 10 O O3 NAG . . . Q 3 -11.635 54.075 86.203 1 148.45 ? O3 NAG 601 D 1 
HETATM 11 O O4 NAG . . . Q 3 -9.948 55.718 87.829 1 154.69 ? O4 NAG 601 D 1 
HETATM 12 O O5 NAG . . . Q 3 -8.506 52.392 88.305 1 154.53 ? O5 NAG 601 D 1 
HETATM 13 O O6 NAG . . . Q 3 -8.589 53.469 90.679 1 138.61 ? O6 NAG 601 D 1 
HETATM 14 O O7 NAG . . . Q 3 -12.657 51.716 85.36 1 134.22 ? O7 NAG 601 D 1 
#
_model_server_stats.io_time_ms              28 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           241 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           14 
#