data_5VDH
#
_model_server_result.job_id            OHL3NlrreLfqzsLYdVUYEg 
_model_server_result.datetime_utc      '2024-12-17 09:32:21' 
_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          5vdh 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"S","auth_seq_id":405}' 
#
_entry.id    5VDH 
#
_exptl.entry_id    5VDH 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          7 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            5VDH 
_cell.length_a            119.065 
_cell.length_b            119.065 
_cell.length_c            429.934 
_cell.Z_PDB               40 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5VDH 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    pentameric 
_pdbx_struct_assembly.oligomeric_count      5 
_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,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA 
_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    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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      7 
_struct_asym.id                             S 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 138 A CYS 138 1_555 A SG CYS 152 A CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? 
disulf ? disulf2 A SG CYS 198 A CYS 198 1_555 A SG CYS 209 A CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? 
disulf ? disulf3 B SG CYS 138 B CYS 138 1_555 B SG CYS 152 B CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
disulf ? disulf4 B SG CYS 198 B CYS 198 1_555 B SG CYS 209 B CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? 
disulf ? disulf5 C SG CYS 138 C CYS 138 1_555 C SG CYS 152 C CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
disulf ? disulf6 C SG CYS 198 C CYS 198 1_555 C SG CYS 209 C CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? 
disulf ? disulf7 D SG CYS 138 D CYS 138 1_555 D SG CYS 152 D CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
disulf ? disulf8 D SG CYS 198 D CYS 198 1_555 D SG CYS 209 D CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? 
disulf ? disulf9 E SG CYS 138 E CYS 138 1_555 E SG CYS 152 E CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
disulf ? disulf10 E SG CYS 198 E CYS 198 1_555 E SG CYS 209 E CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
covale ? covale1 C ND2 ASN 38 C ASN 38 1_555 S C1 NAG . C NAG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
metalc ? metalc1 A OD1 ASP 194 A ASP 194 1_555 I ZN ZN . A ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.552 ? 
metalc ? metalc2 A OD2 ASP 194 A ASP 194 1_555 I ZN ZN . A ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.63 ? 
metalc ? metalc3 B OE2 GLU 192 B GLU 192 1_555 N ZN ZN . B ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? 
metalc ? metalc4 B OD1 ASP 194 B ASP 194 1_555 N ZN ZN . B ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? 
metalc ? metalc5 D OE2 GLU 192 D GLU 192 1_555 W ZN ZN . D ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
metalc ? metalc6 E OE2 GLU 192 E GLU 192 1_555 AA ZN ZN . E ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.556 ? 
#
_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 430 n n 
C1 O1 NAG sing 431 n n 
C1 O5 NAG sing 432 n n 
C1 H1 NAG sing 433 n n 
C2 C3 NAG sing 434 n n 
C2 N2 NAG sing 435 n n 
C2 H2 NAG sing 436 n n 
C3 C4 NAG sing 437 n n 
C3 O3 NAG sing 438 n n 
C3 H3 NAG sing 439 n n 
C4 C5 NAG sing 440 n n 
C4 O4 NAG sing 441 n n 
C4 H4 NAG sing 442 n n 
C5 C6 NAG sing 443 n n 
C5 O5 NAG sing 444 n n 
C5 H5 NAG sing 445 n n 
C6 O6 NAG sing 446 n n 
C6 H61 NAG sing 447 n n 
C6 H62 NAG sing 448 n n 
C7 C8 NAG sing 449 n n 
C7 N2 NAG sing 450 n n 
C7 O7 NAG doub 451 n n 
C8 H81 NAG sing 452 n n 
C8 H82 NAG sing 453 n n 
C8 H83 NAG sing 454 n n 
N2 HN2 NAG sing 455 n n 
O1 HO1 NAG sing 456 n n 
O3 HO3 NAG sing 457 n n 
O4 HO4 NAG sing 458 n n 
O6 HO6 NAG sing 459 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                     5VDH 
_atom_sites.fract_transf_matrix[1][1]    0.008399 
_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]    0.008399 
_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]    0.002326 
_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
F 2 7C6 A 1 401 401 7C6 7C6 . 
G 3 GLY A 1 402 402 GLY GLY . 
H 4 IVM A 1 403 403 IVM IVM . 
I 5 ZN A 1 404 404 ZN ZN . 
J 6 CL A 1 405 405 CL CL . 
K 2 7C6 B 1 401 401 7C6 7C6 . 
L 3 GLY B 1 402 402 GLY GLY . 
M 4 IVM B 1 403 403 IVM IVM . 
N 5 ZN B 1 404 404 ZN ZN . 
O 2 7C6 C 1 401 401 7C6 7C6 . 
P 3 GLY C 1 402 402 GLY GLY . 
Q 4 IVM C 1 403 403 IVM IVM . 
R 5 ZN C 1 404 404 ZN ZN . 
S 7 NAG C 1 405 405 NAG NAG . 
T 2 7C6 D 1 401 401 7C6 7C6 . 
U 3 GLY D 1 402 402 GLY GLY . 
V 4 IVM D 1 403 403 IVM IVM . 
W 5 ZN D 1 404 404 ZN ZN . 
X 2 7C6 E 1 401 401 7C6 7C6 . 
Y 3 GLY E 1 402 402 GLY GLY . 
Z 4 IVM E 1 403 403 IVM IVM . 
AA 5 ZN E 1 404 404 ZN ZN . 
BA 8 HOH A 1 501 501 HOH HOH . 
BA 8 HOH A 2 502 502 HOH HOH . 
BA 8 HOH A 3 503 503 HOH HOH . 
BA 8 HOH A 4 504 504 HOH HOH . 
BA 8 HOH A 5 505 505 HOH HOH . 
BA 8 HOH A 6 506 506 HOH HOH . 
BA 8 HOH A 7 507 507 HOH HOH . 
BA 8 HOH A 8 508 508 HOH HOH . 
BA 8 HOH A 9 509 509 HOH HOH . 
BA 8 HOH A 10 510 510 HOH HOH . 
BA 8 HOH A 11 511 511 HOH HOH . 
BA 8 HOH A 12 512 512 HOH HOH . 
BA 8 HOH A 13 513 513 HOH HOH . 
BA 8 HOH A 14 514 514 HOH HOH . 
BA 8 HOH A 15 515 515 HOH HOH . 
BA 8 HOH A 16 516 516 HOH HOH . 
BA 8 HOH A 17 517 517 HOH HOH . 
BA 8 HOH A 18 518 518 HOH HOH . 
CA 8 HOH B 1 501 501 HOH HOH . 
CA 8 HOH B 2 502 502 HOH HOH . 
CA 8 HOH B 3 503 503 HOH HOH . 
CA 8 HOH B 4 504 504 HOH HOH . 
CA 8 HOH B 5 505 505 HOH HOH . 
CA 8 HOH B 6 506 506 HOH HOH . 
CA 8 HOH B 7 507 507 HOH HOH . 
CA 8 HOH B 8 508 508 HOH HOH . 
CA 8 HOH B 9 509 509 HOH HOH . 
CA 8 HOH B 10 510 510 HOH HOH . 
CA 8 HOH B 11 511 511 HOH HOH . 
DA 8 HOH C 1 501 501 HOH HOH . 
DA 8 HOH C 2 502 502 HOH HOH . 
DA 8 HOH C 3 503 503 HOH HOH . 
DA 8 HOH C 4 504 504 HOH HOH . 
DA 8 HOH C 5 505 505 HOH HOH . 
DA 8 HOH C 6 506 506 HOH HOH . 
DA 8 HOH C 7 507 507 HOH HOH . 
DA 8 HOH C 8 508 508 HOH HOH . 
DA 8 HOH C 9 509 509 HOH HOH . 
DA 8 HOH C 10 510 510 HOH HOH . 
EA 8 HOH D 1 501 501 HOH HOH . 
EA 8 HOH D 2 502 502 HOH HOH . 
EA 8 HOH D 3 503 503 HOH HOH . 
EA 8 HOH D 4 504 504 HOH HOH . 
EA 8 HOH D 5 505 505 HOH HOH . 
EA 8 HOH D 6 506 506 HOH HOH . 
EA 8 HOH D 7 507 507 HOH HOH . 
EA 8 HOH D 8 508 508 HOH HOH . 
FA 8 HOH E 1 501 501 HOH HOH . 
FA 8 HOH E 2 502 502 HOH HOH . 
FA 8 HOH E 3 503 503 HOH HOH . 
FA 8 HOH E 4 504 504 HOH HOH . 
FA 8 HOH E 5 505 505 HOH HOH . 
FA 8 HOH E 6 506 506 HOH HOH . 
FA 8 HOH E 7 507 507 HOH HOH . 
FA 8 HOH E 8 508 508 HOH HOH . 
FA 8 HOH E 9 509 509 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 . . . S 7 505.745 122.768 501.716 1 115.77 ? C1 NAG 405 C 1 
HETATM 2 C C2 NAG . . . S 7 506.76 122.362 502.791 1 121.47 ? C2 NAG 405 C 1 
HETATM 3 C C3 NAG . . . S 7 506.35 121.075 503.511 1 124.78 ? C3 NAG 405 C 1 
HETATM 4 C C4 NAG . . . S 7 504.901 121.133 503.989 1 125.99 ? C4 NAG 405 C 1 
HETATM 5 C C5 NAG . . . S 7 503.995 121.555 502.838 1 123.39 ? C5 NAG 405 C 1 
HETATM 6 C C6 NAG . . . S 7 502.552 121.722 503.313 1 124.97 ? C6 NAG 405 C 1 
HETATM 7 C C7 NAG . . . S 7 509.162 122.873 502.628 1 123.85 ? C7 NAG 405 C 1 
HETATM 8 C C8 NAG . . . S 7 510.461 122.568 501.937 1 123.76 ? C8 NAG 405 C 1 
HETATM 9 N N2 NAG . . . S 7 508.088 122.186 502.22 1 122 ? N2 NAG 405 C 1 
HETATM 10 O O3 NAG . . . S 7 507.203 120.86 504.613 1 127.54 ? O3 NAG 405 C 1 
HETATM 11 O O4 NAG . . . S 7 504.491 119.878 504.495 1 127.04 ? O4 NAG 405 C 1 
HETATM 12 O O5 NAG . . . S 7 504.459 122.783 502.318 1 118.93 ? O5 NAG 405 C 1 
HETATM 13 O O6 NAG . . . S 7 501.808 122.446 502.355 1 124.76 ? O6 NAG 405 C 1 
HETATM 14 O O7 NAG . . . S 7 509.14 123.725 503.517 1 124.27 ? O7 NAG 405 C 1 
#
_model_server_stats.io_time_ms              33 
_model_server_stats.parse_time_ms           23 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           306 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           14 
#