data_6QFY
#
_model_server_result.job_id            zX5x-L9ij1qofz8AQSKRdA 
_model_server_result.datetime_utc      '2024-11-26 01:40:30' 
_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          6qfy 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":504}' 
#
_entry.id    6QFY 
#
_exptl.entry_id    6QFY 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          4 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            2-acetamido-2-deoxy-beta-D-glucopyranose 
_entity.pdbx_number_of_molecules    3 
_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            6QFY 
_cell.length_a            112.572 
_cell.length_b            112.572 
_cell.length_c            141.441 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6QFY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 31 2 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
? monomeric 1 author_defined_assembly 1 
? monomeric 1 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,C,D,H,I,K 1 1 
B,E,F,G,J,L 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
? 4 H N N 
? 4 I N N 
? 4 J 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 
3 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . 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 A 511 NAG 
2 n C NAG 2 C 2 NAG A 512 NAG 
2 n D NAG 1 D 1 NAG A 521 NAG 
2 n D NAG 2 D 2 NAG A 522 NAG 
3 n E NAG 1 E 1 NAG B 501 NAG 
3 n E NAG 2 E 2 NAG B 502 NAG 
3 n E BMA 3 E 3 BMA B 533 BMA 
2 n F NAG 1 F 1 NAG B 521 NAG 
2 n F NAG 2 F 2 NAG B 524 NAG 
2 n G NAG 1 G 1 NAG B 531 NAG 
2 n G NAG 2 G 2 NAG B 532 NAG 
#
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 7 A CYS 21 1_555 A SG CYS 151 A CYS 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? 
disulf ? disulf2 A SG CYS 146 A CYS 160 1_555 A SG CYS 179 A CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? 
disulf ? disulf3 A SG CYS 158 A CYS 172 1_555 A SG CYS 238 A CYS 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? 
disulf ? disulf4 A SG CYS 272 A CYS 286 1_555 A SG CYS 282 A CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? 
disulf ? disulf5 B SG CYS 7 B CYS 21 1_555 B SG CYS 151 B CYS 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? 
disulf ? disulf6 B SG CYS 146 B CYS 160 1_555 B SG CYS 179 B CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? 
disulf ? disulf7 B SG CYS 158 B CYS 172 1_555 B SG CYS 238 B CYS 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? 
disulf ? disulf8 B SG CYS 272 B CYS 286 1_555 B SG CYS 282 B CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? 
covale ? covale1 A ND2 ASN 8 A ASN 22 1_555 H C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? 
covale ? covale2 A ND2 ASN 45 A ASN 59 1_555 I C1 NAG . A NAG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? 
covale ? covale3 A ND2 ASN 119 A ASN 133 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? 
covale ? covale4 A ND2 ASN 184 A ASN 198 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
covale ? covale5 B ND2 ASN 8 B ASN 22 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? 
covale ? covale6 B ND2 ASN 45 B ASN 59 1_555 J C1 NAG . B NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? 
covale ? covale7 B ND2 ASN 119 B ASN 133 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? 
covale ? covale8 B ND2 ASN 184 B ASN 198 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? 
covale ? covale9 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? 
covale ? covale10 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
covale ? covale11 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? 
covale ? covale12 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? 
covale ? covale13 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? 
covale ? covale14 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 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 261 n n 
C1 O1 NAG sing 262 n n 
C1 O5 NAG sing 263 n n 
C1 H1 NAG sing 264 n n 
C2 C3 NAG sing 265 n n 
C2 N2 NAG sing 266 n n 
C2 H2 NAG sing 267 n n 
C3 C4 NAG sing 268 n n 
C3 O3 NAG sing 269 n n 
C3 H3 NAG sing 270 n n 
C4 C5 NAG sing 271 n n 
C4 O4 NAG sing 272 n n 
C4 H4 NAG sing 273 n n 
C5 C6 NAG sing 274 n n 
C5 O5 NAG sing 275 n n 
C5 H5 NAG sing 276 n n 
C6 O6 NAG sing 277 n n 
C6 H61 NAG sing 278 n n 
C6 H62 NAG sing 279 n n 
C7 C8 NAG sing 280 n n 
C7 N2 NAG sing 281 n n 
C7 O7 NAG doub 282 n n 
C8 H81 NAG sing 283 n n 
C8 H82 NAG sing 284 n n 
C8 H83 NAG sing 285 n n 
N2 HN2 NAG sing 286 n n 
O1 HO1 NAG sing 287 n n 
O3 HO3 NAG sing 288 n n 
O4 HO4 NAG sing 289 n n 
O6 HO6 NAG sing 290 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                     6QFY 
_atom_sites.fract_transf_matrix[1][1]    0.008883 
_atom_sites.fract_transf_matrix[1][2]    0.005129 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010257 
_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]    0.00707 
_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
H 4 NAG A 1 501 501 NAG NAG . 
I 4 NAG A 1 506 523 NAG NAG . 
J 4 NAG B 1 504 511 NAG NAG . 
K 5 HOH A 1 601 9 HOH HOH . 
K 5 HOH A 2 602 11 HOH HOH . 
K 5 HOH A 3 603 12 HOH HOH . 
K 5 HOH A 4 604 16 HOH HOH . 
K 5 HOH A 5 605 1 HOH HOH . 
K 5 HOH A 6 606 10 HOH HOH . 
K 5 HOH A 7 607 14 HOH HOH . 
K 5 HOH A 8 608 7 HOH HOH . 
K 5 HOH A 9 609 6 HOH HOH . 
K 5 HOH A 10 610 4 HOH HOH . 
K 5 HOH A 11 611 5 HOH HOH . 
K 5 HOH A 12 612 8 HOH HOH . 
K 5 HOH A 13 613 2 HOH HOH . 
K 5 HOH A 14 614 15 HOH HOH . 
K 5 HOH A 15 615 3 HOH HOH . 
K 5 HOH A 16 616 13 HOH HOH . 
L 5 HOH B 1 601 5 HOH HOH . 
L 5 HOH B 2 602 7 HOH HOH . 
L 5 HOH B 3 603 13 HOH HOH . 
L 5 HOH B 4 604 1 HOH HOH . 
L 5 HOH B 5 605 12 HOH HOH . 
L 5 HOH B 6 606 3 HOH HOH . 
L 5 HOH B 7 607 9 HOH HOH . 
L 5 HOH B 8 608 14 HOH HOH . 
L 5 HOH B 9 609 2 HOH HOH . 
L 5 HOH B 10 610 11 HOH HOH . 
L 5 HOH B 11 611 10 HOH HOH . 
L 5 HOH B 12 612 4 HOH HOH . 
L 5 HOH B 13 613 6 HOH HOH . 
L 5 HOH B 14 614 8 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 C C1 NAG . . . J 4 -26.858 122.257 16.27 1 128.17 ? C1 NAG 504 B 1 
HETATM 2 C C2 NAG . . . J 4 -26.588 123.719 15.871 1 136.81 ? C2 NAG 504 B 1 
HETATM 3 C C3 NAG . . . J 4 -26.354 124.67 17.065 1 135.93 ? C3 NAG 504 B 1 
HETATM 4 C C4 NAG . . . J 4 -27.123 124.315 18.335 1 135.9 ? C4 NAG 504 B 1 
HETATM 5 C C5 NAG . . . J 4 -27.054 122.815 18.593 1 136 ? C5 NAG 504 B 1 
HETATM 6 C C6 NAG . . . J 4 -27.784 122.423 19.874 1 132.43 ? C6 NAG 504 B 1 
HETATM 7 C C7 NAG . . . J 4 -25.355 123.317 13.753 1 146.16 ? C7 NAG 504 B 1 
HETATM 8 C C8 NAG . . . J 4 -24.02 123.453 13.077 1 141.92 ? C8 NAG 504 B 1 
HETATM 9 N N2 NAG . . . J 4 -25.407 123.779 15.008 1 144.73 ? N2 NAG 504 B 1 
HETATM 10 O O3 NAG . . . J 4 -26.711 126.008 16.703 1 133.07 ? O3 NAG 504 B 1 
HETATM 11 O O4 NAG . . . J 4 -26.57 125.046 19.439 1 130.73 ? O4 NAG 504 B 1 
HETATM 12 O O5 NAG . . . J 4 -27.637 122.152 17.469 1 136.36 ? O5 NAG 504 B 1 
HETATM 13 O O6 NAG . . . J 4 -27.137 123.029 20.998 1 130.27 ? O6 NAG 504 B 1 
HETATM 14 O O7 NAG . . . J 4 -26.311 122.811 13.185 1 151.38 ? O7 NAG 504 B 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           259 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           14 
#