data_6YUQ
#
_model_server_result.job_id            bkIszh5bmQdEuEWY_eqa1A 
_model_server_result.datetime_utc      '2024-11-26 23:05:44' 
_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          6yuq 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":407}' 
#
_entry.id    6YUQ 
#
_exptl.entry_id    6YUQ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          6 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            2-acetamido-2-deoxy-alpha-D-mannopyranose 
_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            6YUQ 
_cell.length_a            137.483 
_cell.length_b            137.483 
_cell.length_c            70.253 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6YUQ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    'P 4abw 2nw' 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
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' 8_554 -y,-x,-z-1/2 0 -1 0 -1 0 0 0 0 -1 0 0 -35.1265 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      6 
_struct_asym.id                             I 
_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
covale ? covale1 F O18 BMX . A BMX 404 1_555 G C1 BMX . A BMX 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.359 ? 
covale ? covale2 G O18 BMX . A BMX 405 1_555 H C1 BMX . A BMX 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.378 ? 
covale ? covale3 H O18 BMX . A BMX 406 1_555 I C1 BM3 . A BM3 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.367 ? 
#
_chem_comp.formula           'C8 H15 N O6' 
_chem_comp.formula_weight    221.208 
_chem_comp.id                BM3 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-acetamido-2-deoxy-alpha-D-mannopyranose 
_chem_comp.type              'd-saccharide, alpha linking' 
_chem_comp.pdbx_synonyms     N-acetyl-alpha-D-mannosamine;2-acetamido-2-deoxy-alpha-D-mannose;2-acetamido-2-deoxy-D-mannose;2-acetamido-2-deoxy-mannose;2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-MANNOPYRANOSE 
#
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 O1 BM3 sing 70 n n 
C1 C2 BM3 sing 71 n n 
C1 O5 BM3 sing 72 n n 
C1 H1 BM3 sing 73 n n 
O1 HO1 BM3 sing 74 n n 
C2 N2 BM3 sing 75 n n 
C2 C3 BM3 sing 76 n n 
C2 H2 BM3 sing 77 n n 
N2 C7 BM3 sing 78 n n 
N2 HN2 BM3 sing 79 n n 
C7 O7 BM3 doub 80 n n 
C7 C8 BM3 sing 81 n n 
C8 H81 BM3 sing 82 n n 
C8 H82 BM3 sing 83 n n 
C8 H83 BM3 sing 84 n n 
C3 O3 BM3 sing 85 n n 
C3 C4 BM3 sing 86 n n 
C3 H3 BM3 sing 87 n n 
O3 HO3 BM3 sing 88 n n 
C4 O4 BM3 sing 89 n n 
C4 C5 BM3 sing 90 n n 
C4 H4 BM3 sing 91 n n 
O4 HO4 BM3 sing 92 n n 
C5 C6 BM3 sing 93 n n 
C5 O5 BM3 sing 94 n n 
C5 H5 BM3 sing 95 n n 
C6 O6 BM3 sing 96 n n 
C6 H61 BM3 sing 97 n n 
C6 H62 BM3 sing 98 n n 
O6 HO6 BM3 sing 99 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
BM3 DManpNAca 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 
BM3 N-acetyl-a-D-mannopyranosamine 'COMMON NAME' GMML 1 
BM3 a-D-ManpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 
BM3 ManNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 
#
_atom_sites.entry_id                     6YUQ 
_atom_sites.fract_transf_matrix[1][1]    0.007274 
_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]    0.007274 
_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]    0.014234 
_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 2 EDO A 1 401 401 EDO EDO . 
D 3 PEG A 1 402 501 PEG PEG . 
E 4 CL A 1 403 1 CL CL . 
F 5 BMX A 1 404 301 BMX SV8 . 
G 5 BMX A 1 405 301 BMX SV8 . 
H 5 BMX A 1 406 301 BMX SV8 . 
I 6 BM3 A 1 407 301 BM3 SV8 . 
J 7 PGE B 1 301 301 PGE PGE . 
K 4 CL B 1 302 2 CL CL . 
L 8 HOH A 1 501 1 HOH HOH . 
L 8 HOH A 2 502 36 HOH HOH . 
L 8 HOH A 3 503 9 HOH HOH . 
L 8 HOH A 4 504 4 HOH HOH . 
L 8 HOH A 5 505 7 HOH HOH . 
L 8 HOH A 6 506 14 HOH HOH . 
L 8 HOH A 7 507 40 HOH HOH . 
L 8 HOH A 8 508 30 HOH HOH . 
L 8 HOH A 9 509 17 HOH HOH . 
L 8 HOH A 10 510 29 HOH HOH . 
L 8 HOH A 11 511 15 HOH HOH . 
L 8 HOH A 12 512 24 HOH HOH . 
L 8 HOH A 13 513 38 HOH HOH . 
L 8 HOH A 14 514 12 HOH HOH . 
L 8 HOH A 15 515 35 HOH HOH . 
L 8 HOH A 16 516 21 HOH HOH . 
L 8 HOH A 17 517 34 HOH HOH . 
L 8 HOH A 18 518 33 HOH HOH . 
L 8 HOH A 19 519 10 HOH HOH . 
L 8 HOH A 20 520 25 HOH HOH . 
L 8 HOH A 21 521 18 HOH HOH . 
L 8 HOH A 22 522 26 HOH HOH . 
L 8 HOH A 23 523 47 HOH HOH . 
L 8 HOH A 24 524 45 HOH HOH . 
L 8 HOH A 25 525 32 HOH HOH . 
M 8 HOH B 1 401 42 HOH HOH . 
M 8 HOH B 2 402 20 HOH HOH . 
M 8 HOH B 3 403 28 HOH HOH . 
M 8 HOH B 4 404 5 HOH HOH . 
M 8 HOH B 5 405 22 HOH HOH . 
M 8 HOH B 6 406 27 HOH HOH . 
M 8 HOH B 7 407 13 HOH HOH . 
M 8 HOH B 8 408 6 HOH HOH . 
M 8 HOH B 9 409 2 HOH HOH . 
M 8 HOH B 10 410 41 HOH HOH . 
M 8 HOH B 11 411 37 HOH HOH . 
M 8 HOH B 12 412 31 HOH HOH . 
M 8 HOH B 13 413 19 HOH HOH . 
M 8 HOH B 14 414 3 HOH HOH . 
M 8 HOH B 15 415 8 HOH HOH . 
M 8 HOH B 16 416 23 HOH HOH . 
M 8 HOH B 17 417 11 HOH HOH . 
M 8 HOH B 18 418 46 HOH HOH . 
M 8 HOH B 19 419 16 HOH HOH . 
M 8 HOH B 20 420 44 HOH HOH . 
M 8 HOH B 21 421 39 HOH HOH . 
M 8 HOH B 22 422 43 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 BM3 . . . I 6 -13.798 27.79 -42.7 1 82.98 ? C1 BM3 407 A 1 
HETATM 2 C C2 BM3 . . . I 6 -14.745 28.955 -42.974 1 86.38 ? C2 BM3 407 A 1 
HETATM 3 N N2 BM3 . . . I 6 -14.036 30.146 -43.601 1 86.12 ? N2 BM3 407 A 1 
HETATM 4 C C7 BM3 . . . I 6 -14.608 31.502 -43.42 1 86.68 ? C7 BM3 407 A 1 
HETATM 5 O O7 BM3 . . . I 6 -15.617 31.643 -42.8 1 87.12 ? O7 BM3 407 A 1 
HETATM 6 C C8 BM3 . . . I 6 -13.891 32.746 -44.049 1 89.22 ? C8 BM3 407 A 1 
HETATM 7 C C3 BM3 . . . I 6 -15.875 28.499 -43.809 1 90.73 ? C3 BM3 407 A 1 
HETATM 8 O O3 BM3 . . . I 6 -15.377 28.045 -45.103 1 87.49 ? O3 BM3 407 A 1 
HETATM 9 C C4 BM3 . . . I 6 -16.598 27.364 -43.146 1 90.62 ? C4 BM3 407 A 1 
HETATM 10 O O4 BM3 . . . I 6 -17.948 27.799 -42.929 1 96.81 ? O4 BM3 407 A 1 
HETATM 11 C C5 BM3 . . . I 6 -15.944 26.956 -41.806 1 85.85 ? C5 BM3 407 A 1 
HETATM 12 C C6 BM3 . . . I 6 -16.609 25.734 -41.189 1 81.28 ? C6 BM3 407 A 1 
HETATM 13 O O6 BM3 . . . I 6 -17.536 26.201 -40.231 1 80.21 ? O6 BM3 407 A 1 
HETATM 14 O O5 BM3 . . . I 6 -14.51 26.678 -41.974 1 86.74 ? O5 BM3 407 A 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           27 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           318 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           14 
#