data_6DY1
#
_model_server_result.job_id            4Ebf5G-ID-NFadnkI3D8GQ 
_model_server_result.datetime_utc      '2024-11-15 00:39:49' 
_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          6dy1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":401}' 
#
_entry.id    6DY1 
#
_exptl.entry_id    6DY1 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          3 
_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         90 
_cell.entry_id            6DY1 
_cell.length_a            159.351 
_cell.length_b            159.351 
_cell.length_c            159.351 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6DY1 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        212 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 3 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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
? 3 C N N 
? 3 D N N 
? 3 I 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
covale ? covale1 A ND2 ASN 19 A ASN 39 1_555 C C1 NAG . A NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? 
covale ? covale2 A ND2 ASN 89 A ASN 109 1_555 D C1 NAG . A NAG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? 
covale ? covale3 B ND2 ASN 208 B ASN 335 1_555 I C1 NAG . B NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? 
#
_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 280 n n 
C1 O1 NAG sing 281 n n 
C1 O5 NAG sing 282 n n 
C1 H1 NAG sing 283 n n 
C2 C3 NAG sing 284 n n 
C2 N2 NAG sing 285 n n 
C2 H2 NAG sing 286 n n 
C3 C4 NAG sing 287 n n 
C3 O3 NAG sing 288 n n 
C3 H3 NAG sing 289 n n 
C4 C5 NAG sing 290 n n 
C4 O4 NAG sing 291 n n 
C4 H4 NAG sing 292 n n 
C5 C6 NAG sing 293 n n 
C5 O5 NAG sing 294 n n 
C5 H5 NAG sing 295 n n 
C6 O6 NAG sing 296 n n 
C6 H61 NAG sing 297 n n 
C6 H62 NAG sing 298 n n 
C7 C8 NAG sing 299 n n 
C7 N2 NAG sing 300 n n 
C7 O7 NAG doub 301 n n 
C8 H81 NAG sing 302 n n 
C8 H82 NAG sing 303 n n 
C8 H83 NAG sing 304 n n 
N2 HN2 NAG sing 305 n n 
O1 HO1 NAG sing 306 n n 
O3 HO3 NAG sing 307 n n 
O4 HO4 NAG sing 308 n n 
O6 HO6 NAG sing 309 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                     6DY1 
_atom_sites.fract_transf_matrix[1][1]    0.006275 
_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]    0.006275 
_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]    0.006275 
_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
C 3 NAG A 1 201 1 NAG NAG . 
D 3 NAG A 1 202 2 NAG NAG . 
E 4 SO4 A 1 203 5 SO4 SO4 . 
F 5 CL A 1 204 5 CL CL . 
G 6 TON A 1 205 1 TON TON . 
H 6 TON A 1 206 2 TON TON . 
I 3 NAG B 1 401 3 NAG NAG . 
J 4 SO4 B 1 402 1 SO4 SO4 . 
K 4 SO4 B 1 403 2 SO4 SO4 . 
L 4 SO4 B 1 404 3 SO4 SO4 . 
M 4 SO4 B 1 405 4 SO4 SO4 . 
N 5 CL B 1 406 1 CL CL . 
O 5 CL B 1 407 2 CL CL . 
P 5 CL B 1 408 3 CL CL . 
Q 5 CL B 1 409 4 CL CL . 
R 5 CL B 1 410 6 CL CL . 
S 5 CL B 1 411 7 CL CL . 
T 5 CL B 1 412 8 CL CL . 
U 5 CL B 1 413 9 CL CL . 
V 5 CL B 1 414 10 CL CL . 
W 5 CL B 1 415 11 CL CL . 
X 5 CL B 1 416 12 CL CL . 
Y 7 MYR B 1 417 1 MYR MYR . 
Z 8 HOH A 1 301 16 HOH HOH . 
Z 8 HOH A 2 302 3 HOH HOH . 
Z 8 HOH A 3 303 40 HOH HOH . 
Z 8 HOH A 4 304 5 HOH HOH . 
Z 8 HOH A 5 305 34 HOH HOH . 
Z 8 HOH A 6 306 86 HOH HOH . 
Z 8 HOH A 7 307 63 HOH HOH . 
Z 8 HOH A 8 308 77 HOH HOH . 
Z 8 HOH A 9 309 64 HOH HOH . 
Z 8 HOH A 10 310 32 HOH HOH . 
Z 8 HOH A 11 311 10 HOH HOH . 
Z 8 HOH A 12 312 52 HOH HOH . 
Z 8 HOH A 13 313 41 HOH HOH . 
Z 8 HOH A 14 314 55 HOH HOH . 
Z 8 HOH A 15 315 87 HOH HOH . 
Z 8 HOH A 16 316 20 HOH HOH . 
Z 8 HOH A 17 317 54 HOH HOH . 
Z 8 HOH A 18 318 36 HOH HOH . 
Z 8 HOH A 19 319 17 HOH HOH . 
Z 8 HOH A 20 320 53 HOH HOH . 
Z 8 HOH A 21 321 11 HOH HOH . 
Z 8 HOH A 22 322 68 HOH HOH . 
Z 8 HOH A 23 323 62 HOH HOH . 
Z 8 HOH A 24 324 22 HOH HOH . 
Z 8 HOH A 25 325 70 HOH HOH . 
AA 8 HOH B 1 501 79 HOH HOH . 
AA 8 HOH B 2 502 21 HOH HOH . 
AA 8 HOH B 3 503 6 HOH HOH . 
AA 8 HOH B 4 504 42 HOH HOH . 
AA 8 HOH B 5 505 1 HOH HOH . 
AA 8 HOH B 6 506 78 HOH HOH . 
AA 8 HOH B 7 507 27 HOH HOH . 
AA 8 HOH B 8 508 46 HOH HOH . 
AA 8 HOH B 9 509 15 HOH HOH . 
AA 8 HOH B 10 510 2 HOH HOH . 
AA 8 HOH B 11 511 67 HOH HOH . 
AA 8 HOH B 12 512 43 HOH HOH . 
AA 8 HOH B 13 513 12 HOH HOH . 
AA 8 HOH B 14 514 80 HOH HOH . 
AA 8 HOH B 15 515 9 HOH HOH . 
AA 8 HOH B 16 516 66 HOH HOH . 
AA 8 HOH B 17 517 18 HOH HOH . 
AA 8 HOH B 18 518 4 HOH HOH . 
AA 8 HOH B 19 519 47 HOH HOH . 
AA 8 HOH B 20 520 57 HOH HOH . 
AA 8 HOH B 21 521 60 HOH HOH . 
AA 8 HOH B 22 522 7 HOH HOH . 
AA 8 HOH B 23 523 65 HOH HOH . 
AA 8 HOH B 24 524 13 HOH HOH . 
AA 8 HOH B 25 525 14 HOH HOH . 
AA 8 HOH B 26 526 23 HOH HOH . 
AA 8 HOH B 27 527 76 HOH HOH . 
AA 8 HOH B 28 528 74 HOH HOH . 
AA 8 HOH B 29 529 24 HOH HOH . 
AA 8 HOH B 30 530 33 HOH HOH . 
AA 8 HOH B 31 531 31 HOH HOH . 
AA 8 HOH B 32 532 49 HOH HOH . 
AA 8 HOH B 33 533 84 HOH HOH . 
AA 8 HOH B 34 534 71 HOH HOH . 
AA 8 HOH B 35 535 19 HOH HOH . 
AA 8 HOH B 36 536 48 HOH HOH . 
AA 8 HOH B 37 537 81 HOH HOH . 
AA 8 HOH B 38 538 26 HOH HOH . 
AA 8 HOH B 39 539 44 HOH HOH . 
AA 8 HOH B 40 540 29 HOH HOH . 
AA 8 HOH B 41 541 30 HOH HOH . 
AA 8 HOH B 42 542 82 HOH HOH . 
AA 8 HOH B 43 543 58 HOH HOH . 
AA 8 HOH B 44 544 75 HOH HOH . 
AA 8 HOH B 45 545 37 HOH HOH . 
AA 8 HOH B 46 546 51 HOH HOH . 
AA 8 HOH B 47 547 73 HOH HOH . 
AA 8 HOH B 48 548 25 HOH HOH . 
AA 8 HOH B 49 549 83 HOH HOH . 
AA 8 HOH B 50 550 72 HOH HOH . 
AA 8 HOH B 51 551 45 HOH HOH . 
AA 8 HOH B 52 552 59 HOH HOH . 
AA 8 HOH B 53 553 8 HOH HOH . 
AA 8 HOH B 54 554 56 HOH HOH . 
AA 8 HOH B 55 555 50 HOH HOH . 
AA 8 HOH B 56 556 28 HOH HOH . 
AA 8 HOH B 57 557 89 HOH HOH . 
AA 8 HOH B 58 558 85 HOH HOH . 
AA 8 HOH B 59 559 88 HOH HOH . 
AA 8 HOH B 60 560 61 HOH HOH . 
AA 8 HOH B 61 561 35 HOH HOH . 
AA 8 HOH B 62 562 39 HOH HOH . 
AA 8 HOH B 63 563 38 HOH HOH . 
AA 8 HOH B 64 564 69 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 3 -14.263 30.719 1 1 129.58 ? C1 NAG 401 B 1 
HETATM 2 C C2 NAG . . . I 3 -14.637 31.243 2.393 1 128.62 ? C2 NAG 401 B 1 
HETATM 3 C C3 NAG . . . I 3 -13.987 32.599 2.649 1 130.09 ? C3 NAG 401 B 1 
HETATM 4 C C4 NAG . . . I 3 -12.485 32.519 2.418 1 133.29 ? C4 NAG 401 B 1 
HETATM 5 C C5 NAG . . . I 3 -12.226 32.021 1.003 1 129.95 ? C5 NAG 401 B 1 
HETATM 6 C C6 NAG . . . I 3 -10.758 31.875 0.675 1 112.28 ? C6 NAG 401 B 1 
HETATM 7 C C7 NAG . . . I 3 -16.762 30.709 3.498 1 109.87 ? C7 NAG 401 B 1 
HETATM 8 C C8 NAG . . . I 3 -18.242 30.931 3.503 1 84.6 ? C8 NAG 401 B 1 
HETATM 9 N N2 NAG . . . I 3 -16.079 31.342 2.54 1 132.02 ? N2 NAG 401 B 1 
HETATM 10 O O3 NAG . . . I 3 -14.256 33.007 3.985 1 133.23 ? O3 NAG 401 B 1 
HETATM 11 O O4 NAG . . . I 3 -11.889 33.799 2.599 1 132 ? O4 NAG 401 B 1 
HETATM 12 O O5 NAG . . . I 3 -12.824 30.727 0.845 1 134.79 ? O5 NAG 401 B 1 
HETATM 13 O O6 NAG . . . I 3 -10.1 31.004 1.585 1 82.45 ? O6 NAG 401 B 1 
HETATM 14 O O7 NAG . . . I 3 -16.21 29.984 4.32 1 98.76 ? O7 NAG 401 B 1 
HETATM 15 H H1 NAG . . . I 3 -14.663 31.294 0.321 1 155.49 ? H1 NAG 401 B 1 
HETATM 16 H H2 NAG . . . I 3 -14.299 30.614 3.058 1 154.34 ? H2 NAG 401 B 1 
HETATM 17 H H3 NAG . . . I 3 -14.368 33.255 2.034 1 156.1 ? H3 NAG 401 B 1 
HETATM 18 H H4 NAG . . . I 3 -12.096 31.891 3.056 1 159.94 ? H4 NAG 401 B 1 
HETATM 19 H H5 NAG . . . I 3 -12.634 32.64 0.368 1 155.94 ? H5 NAG 401 B 1 
HETATM 20 H H61 NAG . . . I 3 -10.334 32.753 0.712 1 134.74 ? H61 NAG 401 B 1 
HETATM 21 H H62 NAG . . . I 3 -10.668 31.517 -0.229 1 134.74 ? H62 NAG 401 B 1 
HETATM 22 H H81 NAG . . . I 3 -18.427 31.882 3.62 1 101.52 ? H81 NAG 401 B 1 
HETATM 23 H H82 NAG . . . I 3 -18.644 30.428 4.236 1 101.52 ? H82 NAG 401 B 1 
HETATM 24 H H83 NAG . . . I 3 -18.619 30.628 2.655 1 101.52 ? H83 NAG 401 B 1 
HETATM 25 H HN2 NAG . . . I 3 -16.54 31.87 1.956 1 158.42 ? HN2 NAG 401 B 1 
HETATM 26 H HO3 NAG . . . I 3 -15.123 33.175 4.074 1 159.87 ? HO3 NAG 401 B 1 
HETATM 27 H HO4 NAG . . . I 3 -11.642 33.893 3.447 1 158.4 ? HO4 NAG 401 B 1 
HETATM 28 H HO6 NAG . . . I 3 -9.344 30.714 1.223 1 98.94 ? HO6 NAG 401 B 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           301 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           28 
#