data_5VJK
#
_model_server_result.job_id            PxLsFd-pkko6H3w_nZzg6Q 
_model_server_result.datetime_utc      '2024-12-01 03:53:08' 
_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          5vjk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":502}' 
#
_entry.id    5VJK 
#
_exptl.entry_id    5VJK 
_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    2 
_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            5VJK 
_cell.length_a            115.44 
_cell.length_b            115.44 
_cell.length_c            294.871 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5VJK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        155 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'H 3 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3 
#
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_565 -y,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -57.72 99.973973 0 
3 'crystal symmetry operation' 3_455 -x+y-1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -115.44 0 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 
#
_pdbx_entity_branch.entity_id    3 
_pdbx_entity_branch.type         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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 
2 ? 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
3 n C NAG 1 C 1 NAG B 502 NAG 
3 n C NAG 2 C 2 NAG B 503 NAG 
3 n C BMA 3 C 3 BMA B 504 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 8 A CYS 14 1_555 B SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
disulf ? disulf2 A SG CYS 46 A CYS 52 1_555 A SG CYS 272 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? 
disulf ? disulf3 A SG CYS 58 A CYS 64 1_555 A SG CYS 70 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? 
disulf ? disulf4 A SG CYS 91 A CYS 97 1_555 A SG CYS 133 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? 
disulf ? disulf5 A SG CYS 276 A CYS 281 1_555 A SG CYS 300 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? 
disulf ? disulf6 B SG CYS 144 B CYS 144 1_555 B SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
covale ? covale1 A ND2 ASN 32 A ASN 38 1_555 E C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? 
covale ? covale2 A ND2 ASN 235 A ASN 240 1_555 D C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? 
covale ? covale3 B ND2 ASN 82 B ASN 82 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.468 ? 
covale ? covale4 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? 
covale ? covale5 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? 
#
_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                     5VJK 
_atom_sites.fract_transf_matrix[1][1]    0.008663 
_atom_sites.fract_transf_matrix[1][2]    0.005001 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010003 
_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]    0.003391 
_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 1 501 501 NAG NAG . 
E 4 NAG A 1 502 502 NAG NAG . 
F 5 HOH A 1 601 25 HOH HOH . 
F 5 HOH A 2 602 1 HOH HOH . 
F 5 HOH A 3 603 10 HOH HOH . 
F 5 HOH A 4 604 17 HOH HOH . 
F 5 HOH A 5 605 4 HOH HOH . 
F 5 HOH A 6 606 7 HOH HOH . 
F 5 HOH A 7 607 23 HOH HOH . 
F 5 HOH A 8 608 13 HOH HOH . 
F 5 HOH A 9 609 62 HOH HOH . 
F 5 HOH A 10 610 55 HOH HOH . 
F 5 HOH A 11 611 26 HOH HOH . 
F 5 HOH A 12 612 70 HOH HOH . 
F 5 HOH A 13 613 20 HOH HOH . 
F 5 HOH A 14 614 8 HOH HOH . 
F 5 HOH A 15 615 24 HOH HOH . 
F 5 HOH A 16 616 6 HOH HOH . 
F 5 HOH A 17 617 15 HOH HOH . 
F 5 HOH A 18 618 16 HOH HOH . 
F 5 HOH A 19 619 54 HOH HOH . 
F 5 HOH A 20 620 56 HOH HOH . 
F 5 HOH A 21 621 33 HOH HOH . 
F 5 HOH A 22 622 41 HOH HOH . 
F 5 HOH A 23 623 48 HOH HOH . 
F 5 HOH A 24 624 45 HOH HOH . 
F 5 HOH A 25 625 50 HOH HOH . 
F 5 HOH A 26 626 66 HOH HOH . 
F 5 HOH A 27 627 27 HOH HOH . 
F 5 HOH A 28 628 69 HOH HOH . 
F 5 HOH A 29 629 14 HOH HOH . 
F 5 HOH A 30 630 12 HOH HOH . 
F 5 HOH A 31 631 22 HOH HOH . 
F 5 HOH A 32 632 21 HOH HOH . 
F 5 HOH A 33 633 67 HOH HOH . 
F 5 HOH A 34 634 71 HOH HOH . 
F 5 HOH A 35 635 44 HOH HOH . 
F 5 HOH A 36 636 42 HOH HOH . 
F 5 HOH A 37 637 38 HOH HOH . 
F 5 HOH A 38 638 31 HOH HOH . 
F 5 HOH A 39 639 37 HOH HOH . 
F 5 HOH A 40 640 39 HOH HOH . 
F 5 HOH A 41 641 59 HOH HOH . 
F 5 HOH A 42 642 43 HOH HOH . 
F 5 HOH A 43 643 47 HOH HOH . 
F 5 HOH A 44 644 40 HOH HOH . 
F 5 HOH A 45 645 46 HOH HOH . 
F 5 HOH A 46 646 53 HOH HOH . 
F 5 HOH A 47 647 61 HOH HOH . 
F 5 HOH A 48 648 60 HOH HOH . 
G 5 HOH B 1 301 2 HOH HOH . 
G 5 HOH B 2 302 19 HOH HOH . 
G 5 HOH B 3 303 29 HOH HOH . 
G 5 HOH B 4 304 5 HOH HOH . 
G 5 HOH B 5 305 34 HOH HOH . 
G 5 HOH B 6 306 9 HOH HOH . 
G 5 HOH B 7 307 30 HOH HOH . 
G 5 HOH B 8 308 18 HOH HOH . 
G 5 HOH B 9 309 49 HOH HOH . 
G 5 HOH B 10 310 58 HOH HOH . 
G 5 HOH B 11 311 3 HOH HOH . 
G 5 HOH B 12 312 36 HOH HOH . 
G 5 HOH B 13 313 68 HOH HOH . 
G 5 HOH B 14 314 51 HOH HOH . 
G 5 HOH B 15 315 35 HOH HOH . 
G 5 HOH B 16 316 11 HOH HOH . 
G 5 HOH B 17 317 65 HOH HOH . 
G 5 HOH B 18 318 32 HOH HOH . 
G 5 HOH B 19 319 64 HOH HOH . 
G 5 HOH B 20 320 52 HOH HOH . 
G 5 HOH B 21 321 63 HOH HOH . 
G 5 HOH B 22 322 28 HOH HOH . 
G 5 HOH B 23 323 57 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 . . . E 4 -44.801 14.179 32.515 1 132.35 ? C1 NAG 502 A 1 
HETATM 2 C C2 NAG . . . E 4 -45.138 12.769 32.982 1 134.68 ? C2 NAG 502 A 1 
HETATM 3 C C3 NAG . . . E 4 -45.281 11.838 31.789 1 138.64 ? C3 NAG 502 A 1 
HETATM 4 C C4 NAG . . . E 4 -46.401 12.325 30.884 1 139.01 ? C4 NAG 502 A 1 
HETATM 5 C C5 NAG . . . E 4 -46.115 13.747 30.402 1 138.1 ? C5 NAG 502 A 1 
HETATM 6 C C6 NAG . . . E 4 -47.299 14.344 29.685 1 136.57 ? C6 NAG 502 A 1 
HETATM 7 C C7 NAG . . . E 4 -44.266 12.392 35.221 1 115.35 ? C7 NAG 502 A 1 
HETATM 8 C C8 NAG . . . E 4 -43.166 11.81 36.048 1 104.25 ? C8 NAG 502 A 1 
HETATM 9 N N2 NAG . . . E 4 -44.136 12.265 33.903 1 127.9 ? N2 NAG 502 A 1 
HETATM 10 O O3 NAG . . . E 4 -45.581 10.532 32.268 1 140.82 ? O3 NAG 502 A 1 
HETATM 11 O O4 NAG . . . E 4 -46.567 11.435 29.782 1 136.69 ? O4 NAG 502 A 1 
HETATM 12 O O5 NAG . . . E 4 -45.818 14.632 31.502 1 136.24 ? O5 NAG 502 A 1 
HETATM 13 O O6 NAG . . . E 4 -48.281 14.791 30.609 1 131.4 ? O6 NAG 502 A 1 
HETATM 14 O O7 NAG . . . E 4 -45.234 12.955 35.718 1 114.23 ? O7 NAG 502 A 1 
#
_model_server_stats.io_time_ms              59 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    17 
_model_server_stats.query_time_ms           340 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           14 
#