data_3VN4
#
_model_server_result.job_id            GGOXfxcH0jG7qTdJ_DHcbg 
_model_server_result.datetime_utc      '2025-02-05 18:07:30' 
_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          3vn4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":701}' 
#
_entry.id    3VN4 
#
_exptl.entry_id    3VN4 
_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    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          111.56 
_cell.angle_gamma         90 
_cell.entry_id            3VN4 
_cell.length_a            153.378 
_cell.length_b            53.243 
_cell.length_c            76.615 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3VN4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 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 
PISA dimeric 2 software_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,C,D,E,F 1 1 
A,B,C,D,E,F 2 1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 BGC FUC C1 O1 . O3 HO3 . 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 A 901 NAG 
2 n B NAG 2 B 2 NAG A 902 NAG 
3 n C FUC 1 C 1 FUC A 903 FUC 
3 n C BGC 2 C 2 BGC A 904 BGC 
#
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 27 A CYS 311 1_555 A SG CYS 53 A CYS 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf2 A SG CYS 38 A CYS 322 1_555 A SG CYS 63 A CYS 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf3 A SG CYS 48 A CYS 332 1_555 A SG CYS 82 A CYS 366 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf4 A SG CYS 76 A CYS 360 1_555 A SG CYS 87 A CYS 371 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf5 A SG CYS 112 A CYS 396 1_555 A SG CYS 149 A CYS 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf6 A SG CYS 116 A CYS 400 1_555 A SG CYS 154 A CYS 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf7 A SG CYS 127 A CYS 411 1_555 A SG CYS 139 A CYS 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf8 A SG CYS 166 A CYS 450 1_555 A SG CYS 203 A CYS 487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
disulf ? disulf9 A SG CYS 199 A CYS 483 1_555 A SG CYS 238 A CYS 522 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf10 A SG CYS 224 A CYS 508 1_555 A SG CYS 243 A CYS 527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf11 A SG CYS 248 A CYS 532 1_555 A SG CYS 264 A CYS 548 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? 
disulf ? disulf12 A SG CYS 261 A CYS 545 1_555 A SG CYS 271 A CYS 555 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? 
covale ? covale1 A CD1 TRP 103 A TRP 387 1_555 E C1 MAN . A MAN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.48 ? 
covale ? covale2 A OG SER 115 A SER 399 1_555 C C1 FUC . C FUC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? 
covale ? covale3 A ND2 ASN 268 A ASN 552 1_555 D C1 NAG . A NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
covale ? covale4 A ND2 ASN 330 A ASN 614 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
covale ? covale5 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? 
covale ? covale6 C O3 FUC . C FUC 1 1_555 C C1 BGC . C BGC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? 
#
_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 308 n n 
C1 O1 NAG sing 309 n n 
C1 O5 NAG sing 310 n n 
C1 H1 NAG sing 311 n n 
C2 C3 NAG sing 312 n n 
C2 N2 NAG sing 313 n n 
C2 H2 NAG sing 314 n n 
C3 C4 NAG sing 315 n n 
C3 O3 NAG sing 316 n n 
C3 H3 NAG sing 317 n n 
C4 C5 NAG sing 318 n n 
C4 O4 NAG sing 319 n n 
C4 H4 NAG sing 320 n n 
C5 C6 NAG sing 321 n n 
C5 O5 NAG sing 322 n n 
C5 H5 NAG sing 323 n n 
C6 O6 NAG sing 324 n n 
C6 H61 NAG sing 325 n n 
C6 H62 NAG sing 326 n n 
C7 C8 NAG sing 327 n n 
C7 N2 NAG sing 328 n n 
C7 O7 NAG doub 329 n n 
C8 H81 NAG sing 330 n n 
C8 H82 NAG sing 331 n n 
C8 H83 NAG sing 332 n n 
N2 HN2 NAG sing 333 n n 
O1 HO1 NAG sing 334 n n 
O3 HO3 NAG sing 335 n n 
O4 HO4 NAG sing 336 n n 
O6 HO6 NAG sing 337 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                     3VN4 
_atom_sites.fract_transf_matrix[1][1]    0.00652 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002576 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.018782 
_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]    0.014034 
_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 1 701 900 NAG NAG . 
E 5 MAN A 1 702 905 MAN BMA . 
F 6 HOH A 1 1001 1 HOH HOH . 
F 6 HOH A 2 1002 26 HOH HOH . 
F 6 HOH A 3 1003 18 HOH HOH . 
F 6 HOH A 4 1004 25 HOH HOH . 
F 6 HOH A 5 1005 37 HOH HOH . 
F 6 HOH A 6 1006 40 HOH HOH . 
F 6 HOH A 7 1007 6 HOH HOH . 
F 6 HOH A 8 1008 20 HOH HOH . 
F 6 HOH A 9 1009 2 HOH HOH . 
F 6 HOH A 10 1010 16 HOH HOH . 
F 6 HOH A 11 1011 36 HOH HOH . 
F 6 HOH A 12 1012 13 HOH HOH . 
F 6 HOH A 13 1013 19 HOH HOH . 
F 6 HOH A 14 1014 14 HOH HOH . 
F 6 HOH A 15 1015 5 HOH HOH . 
F 6 HOH A 16 1016 34 HOH HOH . 
F 6 HOH A 17 1017 23 HOH HOH . 
F 6 HOH A 18 1018 42 HOH HOH . 
F 6 HOH A 19 1019 3 HOH HOH . 
F 6 HOH A 20 1020 28 HOH HOH . 
F 6 HOH A 21 1021 33 HOH HOH . 
F 6 HOH A 22 1022 45 HOH HOH . 
F 6 HOH A 23 1023 29 HOH HOH . 
F 6 HOH A 24 1024 4 HOH HOH . 
F 6 HOH A 25 1025 35 HOH HOH . 
F 6 HOH A 26 1026 8 HOH HOH . 
F 6 HOH A 27 1027 24 HOH HOH . 
F 6 HOH A 28 1028 17 HOH HOH . 
F 6 HOH A 29 1029 44 HOH HOH . 
F 6 HOH A 30 1030 7 HOH HOH . 
F 6 HOH A 31 1031 43 HOH HOH . 
F 6 HOH A 32 1032 22 HOH HOH . 
F 6 HOH A 33 1033 9 HOH HOH . 
F 6 HOH A 34 1034 12 HOH HOH . 
F 6 HOH A 35 1035 38 HOH HOH . 
F 6 HOH A 36 1036 15 HOH HOH . 
F 6 HOH A 37 1037 39 HOH HOH . 
F 6 HOH A 38 1038 31 HOH HOH . 
F 6 HOH A 39 1039 10 HOH HOH . 
F 6 HOH A 40 1040 30 HOH HOH . 
F 6 HOH A 41 1041 21 HOH HOH . 
F 6 HOH A 42 1042 41 HOH HOH . 
F 6 HOH A 43 1043 11 HOH HOH . 
F 6 HOH A 44 1044 32 HOH HOH . 
F 6 HOH A 45 1045 27 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 . . . D 4 29.668 8.83 -7.389 1 68.36 ? C1 NAG 701 A 1 
HETATM 2 C C2 NAG . . . D 4 28.721 8.071 -8.309 1 71.63 ? C2 NAG 701 A 1 
HETATM 3 C C3 NAG . . . D 4 27.314 8.224 -7.754 1 71.81 ? C3 NAG 701 A 1 
HETATM 4 C C4 NAG . . . D 4 27.27 7.634 -6.351 1 71.69 ? C4 NAG 701 A 1 
HETATM 5 C C5 NAG . . . D 4 28.453 8.059 -5.469 1 71.33 ? C5 NAG 701 A 1 
HETATM 6 C C6 NAG . . . D 4 28.593 7.078 -4.306 1 71.49 ? C6 NAG 701 A 1 
HETATM 7 C C7 NAG . . . D 4 29.521 7.812 -10.624 1 75 ? C7 NAG 701 A 1 
HETATM 8 C C8 NAG . . . D 4 30.215 6.537 -10.215 1 75.21 ? C8 NAG 701 A 1 
HETATM 9 N N2 NAG . . . D 4 28.832 8.497 -9.698 1 73.2 ? N2 NAG 701 A 1 
HETATM 10 O O3 NAG . . . D 4 26.389 7.545 -8.571 1 72.38 ? O3 NAG 701 A 1 
HETATM 11 O O4 NAG . . . D 4 26.053 8.008 -5.739 1 72.23 ? O4 NAG 701 A 1 
HETATM 12 O O5 NAG . . . D 4 29.695 8.115 -6.164 1 70.17 ? O5 NAG 701 A 1 
HETATM 13 O O6 NAG . . . D 4 29.457 7.602 -3.326 1 71.9 ? O6 NAG 701 A 1 
HETATM 14 O O7 NAG . . . D 4 29.605 8.194 -11.794 1 76.07 ? O7 NAG 701 A 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           280 
_model_server_stats.encode_time_ms          20 
_model_server_stats.element_count           14 
#