data_6IDZ
#
_model_server_result.job_id            '_spZYqY_LBlIfT0azlMg4Q' 
_model_server_result.datetime_utc      '2024-10-17 10:12:52' 
_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          6idz 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":401}' 
#
_entry.id    6IDZ 
#
_exptl.entry_id    6IDZ 
_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            6IDZ 
_cell.length_a            116.101 
_cell.length_b            116.101 
_cell.length_c            296.275 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6IDZ 
_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_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 
3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 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 GAL NAG C1 O1 . O4 HO4 . sing 
2 ? 3 3 2 SIA GAL C2 O2 . 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
3 n C NAG 1 C 1 NAG A 404 NAG 
3 n C GAL 2 C 2 GAL A 403 GAL 
3 n C SIA 3 C 3 SIA A 402 SIA 
#
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 4 A CYS 4 1_555 B SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf2 A SG CYS 42 A CYS 42 1_555 A SG CYS 268 A CYS 268 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf3 A SG CYS 54 A CYS 54 1_555 A SG CYS 66 A CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf4 A SG CYS 87 A CYS 87 1_555 A SG CYS 129 A CYS 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf5 A SG CYS 272 A CYS 272 1_555 A SG CYS 296 A CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf6 B SG CYS 144 B CYS 144 1_555 B SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
covale ? covale1 A ND2 ASN 28 A ASN 28 1_555 D C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
covale ? covale2 B ND2 ASN 82 B ASN 82 1_555 E C1 NAG . B NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
covale ? covale3 C O4 NAG . C NAG 1 1_555 C C1 GAL . C GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? 
covale ? covale4 C O3 GAL . C GAL 2 1_555 C C2 SIA . C SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.477 ? 
#
_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                     6IDZ 
_atom_sites.fract_transf_matrix[1][1]    0.008613 
_atom_sites.fract_transf_matrix[1][2]    0.004973 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009946 
_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]    0.003375 
_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 1 401 401 NAG NAG . 
E 4 NAG B 1 201 201 NAG NAG . 
F 5 HOH A 1 501 501 HOH HOH . 
F 5 HOH A 2 502 502 HOH HOH . 
F 5 HOH A 3 503 503 HOH HOH . 
F 5 HOH A 4 504 504 HOH HOH . 
F 5 HOH A 5 505 505 HOH HOH . 
F 5 HOH A 6 506 506 HOH HOH . 
F 5 HOH A 7 507 507 HOH HOH . 
F 5 HOH A 8 508 508 HOH HOH . 
F 5 HOH A 9 509 509 HOH HOH . 
F 5 HOH A 10 510 510 HOH HOH . 
F 5 HOH A 11 511 511 HOH HOH . 
F 5 HOH A 12 512 512 HOH HOH . 
F 5 HOH A 13 513 513 HOH HOH . 
F 5 HOH A 14 514 514 HOH HOH . 
F 5 HOH A 15 515 515 HOH HOH . 
F 5 HOH A 16 516 516 HOH HOH . 
F 5 HOH A 17 517 517 HOH HOH . 
F 5 HOH A 18 518 519 HOH HOH . 
F 5 HOH A 19 519 520 HOH HOH . 
F 5 HOH A 20 520 521 HOH HOH . 
F 5 HOH A 21 521 522 HOH HOH . 
F 5 HOH A 22 522 524 HOH HOH . 
F 5 HOH A 23 523 525 HOH HOH . 
F 5 HOH A 24 524 526 HOH HOH . 
F 5 HOH A 25 525 527 HOH HOH . 
F 5 HOH A 26 526 528 HOH HOH . 
F 5 HOH A 27 527 529 HOH HOH . 
F 5 HOH A 28 528 530 HOH HOH . 
F 5 HOH A 29 529 531 HOH HOH . 
F 5 HOH A 30 530 532 HOH HOH . 
F 5 HOH A 31 531 533 HOH HOH . 
F 5 HOH A 32 532 534 HOH HOH . 
F 5 HOH A 33 533 535 HOH HOH . 
F 5 HOH A 34 534 536 HOH HOH . 
F 5 HOH A 35 535 537 HOH HOH . 
F 5 HOH A 36 536 538 HOH HOH . 
F 5 HOH A 37 537 539 HOH HOH . 
F 5 HOH A 38 538 540 HOH HOH . 
F 5 HOH A 39 539 541 HOH HOH . 
F 5 HOH A 40 540 542 HOH HOH . 
F 5 HOH A 41 541 543 HOH HOH . 
F 5 HOH A 42 542 544 HOH HOH . 
F 5 HOH A 43 543 545 HOH HOH . 
F 5 HOH A 44 544 546 HOH HOH . 
F 5 HOH A 45 545 547 HOH HOH . 
F 5 HOH A 46 546 548 HOH HOH . 
F 5 HOH A 47 547 549 HOH HOH . 
F 5 HOH A 48 548 550 HOH HOH . 
F 5 HOH A 49 549 551 HOH HOH . 
F 5 HOH A 50 550 552 HOH HOH . 
F 5 HOH A 51 551 553 HOH HOH . 
F 5 HOH A 52 552 554 HOH HOH . 
F 5 HOH A 53 553 555 HOH HOH . 
F 5 HOH A 54 554 556 HOH HOH . 
F 5 HOH A 55 555 557 HOH HOH . 
F 5 HOH A 56 556 558 HOH HOH . 
F 5 HOH A 57 557 559 HOH HOH . 
F 5 HOH A 58 558 560 HOH HOH . 
F 5 HOH A 59 559 561 HOH HOH . 
F 5 HOH A 60 560 562 HOH HOH . 
G 5 HOH B 1 301 301 HOH HOH . 
G 5 HOH B 2 302 302 HOH HOH . 
G 5 HOH B 3 303 303 HOH HOH . 
G 5 HOH B 4 304 304 HOH HOH . 
G 5 HOH B 5 305 305 HOH HOH . 
G 5 HOH B 6 306 306 HOH HOH . 
G 5 HOH B 7 307 307 HOH HOH . 
G 5 HOH B 8 308 308 HOH HOH . 
G 5 HOH B 9 309 310 HOH HOH . 
G 5 HOH B 10 310 311 HOH HOH . 
G 5 HOH B 11 311 312 HOH HOH . 
G 5 HOH B 12 312 313 HOH HOH . 
G 5 HOH B 13 313 314 HOH HOH . 
G 5 HOH B 14 314 315 HOH HOH . 
G 5 HOH B 15 315 316 HOH HOH . 
G 5 HOH B 16 316 317 HOH HOH . 
G 5 HOH B 17 317 318 HOH HOH . 
G 5 HOH B 18 318 319 HOH HOH . 
G 5 HOH B 19 319 321 HOH HOH . 
G 5 HOH B 20 320 322 HOH HOH . 
G 5 HOH B 21 321 323 HOH HOH . 
G 5 HOH B 22 322 324 HOH HOH . 
G 5 HOH B 23 323 325 HOH HOH . 
G 5 HOH B 24 324 326 HOH HOH . 
G 5 HOH B 25 325 327 HOH HOH . 
G 5 HOH B 26 326 328 HOH HOH . 
G 5 HOH B 27 327 329 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 10.9 19.841 81.845 1 85.21 ? C1 NAG 401 A 1 
HETATM 2 C C2 NAG . . . D 4 12.152 20.406 82.519 1 87.73 ? C2 NAG 401 A 1 
HETATM 3 C C3 NAG . . . D 4 13.217 20.738 81.477 1 84.26 ? C3 NAG 401 A 1 
HETATM 4 C C4 NAG . . . D 4 13.498 19.527 80.598 1 83.1 ? C4 NAG 401 A 1 
HETATM 5 C C5 NAG . . . D 4 12.198 19.022 79.982 1 80.12 ? C5 NAG 401 A 1 
HETATM 6 C C6 NAG . . . D 4 12.378 17.76 79.173 1 72.63 ? C6 NAG 401 A 1 
HETATM 7 C C7 NAG . . . D 4 12.184 21.721 84.591 1 81.1 ? C7 NAG 401 A 1 
HETATM 8 C C8 NAG . . . D 4 11.766 22.999 85.254 1 71.61 ? C8 NAG 401 A 1 
HETATM 9 N N2 NAG . . . D 4 11.829 21.582 83.31 1 88.15 ? N2 NAG 401 A 1 
HETATM 10 O O3 NAG . . . D 4 14.411 21.144 82.137 1 78.12 ? O3 NAG 401 A 1 
HETATM 11 O O4 NAG . . . D 4 14.413 19.873 79.564 1 76.71 ? O4 NAG 401 A 1 
HETATM 12 O O5 NAG . . . D 4 11.257 18.716 81.022 1 84.27 ? O5 NAG 401 A 1 
HETATM 13 O O6 NAG . . . D 4 12.351 16.605 80.001 1 71 ? O6 NAG 401 A 1 
HETATM 14 O O7 NAG . . . D 4 12.816 20.854 85.188 1 73.06 ? O7 NAG 401 A 1 
#
_model_server_stats.io_time_ms              62 
_model_server_stats.parse_time_ms           27 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           290 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           14 
#