data_4YDI
#
_model_server_result.job_id            MBM7GlcLZS1HB7mPrHlfTg 
_model_server_result.datetime_utc      '2024-11-23 13:54:21' 
_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          4ydi 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":506}' 
#
_entry.id    4YDI 
#
_exptl.entry_id    4YDI 
_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    13 
_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            4YDI 
_cell.length_a            141.738 
_cell.length_b            172.253 
_cell.length_c            91.782 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4YDI 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        21 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 2 2 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_pdbx_struct_assembly.details               author_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 
_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 
#
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 
? 4 F N N 
? 4 G N N 
? 4 H N N 
? 4 I N N 
? 4 J N N 
? 4 K N N 
? 4 L N N 
? 4 M N N 
? 4 N N N 
? 4 O N N 
? 4 U 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 11 G CYS 54 1_555 A SG CYS 31 G CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? 
disulf ? disulf2 A SG CYS 76 G CYS 119 1_555 A SG CYS 89 G CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf3 A SG CYS 102 G CYS 218 1_555 A SG CYS 131 G CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf4 A SG CYS 112 G CYS 228 1_555 A SG CYS 123 G CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf5 A SG CYS 180 G CYS 296 1_555 A SG CYS 199 G CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf6 A SG CYS 245 G CYS 378 1_555 A SG CYS 312 G CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
disulf ? disulf7 A SG CYS 252 G CYS 385 1_555 A SG CYS 285 G CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? 
disulf ? disulf8 B SG CYS 22 H CYS 22 1_555 B SG CYS 96 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
disulf ? disulf9 B SG CYS 149 H CYS 140 1_555 B SG CYS 205 H CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf10 C SG CYS 23 L CYS 23 1_555 C SG CYS 88 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf11 C SG CYS 130 L CYS 134 1_555 C SG CYS 190 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
covale ? covale1 A ND2 ASN 118 G ASN 234 1_555 D C1 NAG . G NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
covale ? covale2 A ND2 ASN 125 G ASN 241 1_555 E C1 NAG . G NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? 
covale ? covale3 A ND2 ASN 146 G ASN 262 1_555 F C1 NAG . G NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? 
covale ? covale4 A ND2 ASN 160 G ASN 276 1_555 G C1 NAG . G NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? 
covale ? covale5 A ND2 ASN 200 G ASN 332 1_555 H C1 NAG . G NAG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? 
covale ? covale6 A ND2 ASN 223 G ASN 355 1_555 M C1 NAG . G NAG 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? 
covale ? covale7 A ND2 ASN 230 G ASN 363 1_555 I C1 NAG . G NAG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? 
covale ? covale8 A ND2 ASN 253 G ASN 386 1_555 J C1 NAG . G NAG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? 
covale ? covale9 A ND2 ASN 259 G ASN 392 1_555 K C1 NAG . G NAG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? 
covale ? covale10 A ND2 ASN 265 G ASN 398 1_555 N C1 NAG . G NAG 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? 
covale ? covale11 A ND2 ASN 315 G ASN 448 1_555 L C1 NAG . G NAG 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
covale ? covale12 A ND2 ASN 332 G ASN 465 1_555 O C1 NAG . G NAG 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
covale ? covale13 C ND2 ASN 103 L ASN 107 1_555 U C1 NAG . L NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
#
_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 246 n n 
C1 O1 NAG sing 247 n n 
C1 O5 NAG sing 248 n n 
C1 H1 NAG sing 249 n n 
C2 C3 NAG sing 250 n n 
C2 N2 NAG sing 251 n n 
C2 H2 NAG sing 252 n n 
C3 C4 NAG sing 253 n n 
C3 O3 NAG sing 254 n n 
C3 H3 NAG sing 255 n n 
C4 C5 NAG sing 256 n n 
C4 O4 NAG sing 257 n n 
C4 H4 NAG sing 258 n n 
C5 C6 NAG sing 259 n n 
C5 O5 NAG sing 260 n n 
C5 H5 NAG sing 261 n n 
C6 O6 NAG sing 262 n n 
C6 H61 NAG sing 263 n n 
C6 H62 NAG sing 264 n n 
C7 C8 NAG sing 265 n n 
C7 N2 NAG sing 266 n n 
C7 O7 NAG doub 267 n n 
C8 H81 NAG sing 268 n n 
C8 H82 NAG sing 269 n n 
C8 H83 NAG sing 270 n n 
N2 HN2 NAG sing 271 n n 
O1 HO1 NAG sing 272 n n 
O3 HO3 NAG sing 273 n n 
O4 HO4 NAG sing 274 n n 
O6 HO6 NAG sing 275 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                     4YDI 
_atom_sites.fract_transf_matrix[1][1]    0.007055 
_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]    0.005805 
_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]    0.010895 
_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 G 1 501 734 NAG NAG . 
E 4 NAG G 1 502 741 NAG NAG . 
F 4 NAG G 1 503 762 NAG NAG . 
G 4 NAG G 1 504 776 NAG NAG . 
H 4 NAG G 1 505 832 NAG NAG . 
I 4 NAG G 1 506 863 NAG NAG . 
J 4 NAG G 1 507 886 NAG NAG . 
K 4 NAG G 1 508 892 NAG NAG . 
L 4 NAG G 1 509 948 NAG NAG . 
M 4 NAG G 1 510 855 NAG NAG . 
N 4 NAG G 1 511 898 NAG NAG . 
O 4 NAG G 1 512 965 NAG NAG . 
P 5 SO4 G 1 513 1 SO4 SO4 . 
Q 5 SO4 H 1 301 2 SO4 SO4 . 
R 5 SO4 H 1 302 3 SO4 SO4 . 
S 6 EDO H 1 303 4 EDO EDO . 
T 5 SO4 H 1 304 7 SO4 SO4 . 
U 4 NAG L 1 301 607 NAG NAG . 
V 7 HOH G 1 601 25 HOH HOH . 
V 7 HOH G 2 602 32 HOH HOH . 
V 7 HOH G 3 603 40 HOH HOH . 
V 7 HOH G 4 604 29 HOH HOH . 
V 7 HOH G 5 605 42 HOH HOH . 
V 7 HOH G 6 606 20 HOH HOH . 
V 7 HOH G 7 607 47 HOH HOH . 
V 7 HOH G 8 608 41 HOH HOH . 
V 7 HOH G 9 609 27 HOH HOH . 
W 7 HOH H 1 401 24 HOH HOH . 
W 7 HOH H 2 402 45 HOH HOH . 
W 7 HOH H 3 403 37 HOH HOH . 
W 7 HOH H 4 404 31 HOH HOH . 
W 7 HOH H 5 405 19 HOH HOH . 
W 7 HOH H 6 406 44 HOH HOH . 
W 7 HOH H 7 407 46 HOH HOH . 
W 7 HOH H 8 408 26 HOH HOH . 
X 7 HOH L 1 401 43 HOH HOH . 
X 7 HOH L 2 402 18 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 . . . I 4 -36.486 -12.166 1.812 1 111.07 ? C1 NAG 506 G 1 
HETATM 2 C C2 NAG . . . I 4 -37.16 -10.934 1.194 1 110.73 ? C2 NAG 506 G 1 
HETATM 3 C C3 NAG . . . I 4 -37.102 -11.003 -0.333 1 113.25 ? C3 NAG 506 G 1 
HETATM 4 C C4 NAG . . . I 4 -35.677 -11.251 -0.809 1 112.33 ? C4 NAG 506 G 1 
HETATM 5 C C5 NAG . . . I 4 -35.111 -12.485 -0.116 1 115.46 ? C5 NAG 506 G 1 
HETATM 6 C C6 NAG . . . I 4 -33.673 -12.774 -0.481 1 119.09 ? C6 NAG 506 G 1 
HETATM 7 C C7 NAG . . . I 4 -38.995 -9.78 2.359 1 101.41 ? C7 NAG 506 G 1 
HETATM 8 C C8 NAG . . . I 4 -40.447 -9.829 2.731 1 101.24 ? C8 NAG 506 G 1 
HETATM 9 N N2 NAG . . . I 4 -38.538 -10.815 1.646 1 106.01 ? N2 NAG 506 G 1 
HETATM 10 O O3 NAG . . . I 4 -37.592 -9.784 -0.882 1 118 ? O3 NAG 506 G 1 
HETATM 11 O O4 NAG . . . I 4 -35.663 -11.453 -2.217 1 110.45 ? O4 NAG 506 G 1 
HETATM 12 O O5 NAG . . . I 4 -35.156 -12.295 1.306 1 112.53 ? O5 NAG 506 G 1 
HETATM 13 O O6 NAG . . . I 4 -33.541 -14.056 -1.081 1 117.66 ? O6 NAG 506 G 1 
HETATM 14 O O7 NAG . . . I 4 -38.271 -8.848 2.692 1 104.33 ? O7 NAG 506 G 1 
#
_model_server_stats.io_time_ms              25 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    19 
_model_server_stats.query_time_ms           686 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           14 
#