data_6XPX
#
_model_server_result.job_id            e5YVPguaPsaDhjo3DJepHQ 
_model_server_result.datetime_utc      '2024-11-30 11:55:22' 
_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          6xpx 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":402}' 
#
_entry.id    6XPX 
#
_exptl.entry_id    6XPX 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          5 
_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          108.01 
_cell.angle_gamma         90 
_cell.entry_id            6XPX 
_cell.length_a            68.42 
_cell.length_b            101.56 
_cell.length_c            77.41 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6XPX 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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 
_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
? 5 E N N 
? 5 F N N 
#
_pdbx_entity_branch.entity_id    4 
_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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 
2 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . 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
4 n D NAG 1 D 1 NAG A 802 NAG 
4 n D NAG 2 D 2 NAG A 803 NAG 
4 n D BMA 3 D 3 BMA A 804 BMA 
#
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 16 A CYS 52 1_555 A SG CYS 241 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? 
disulf ? disulf2 A SG CYS 28 A CYS 64 1_555 A SG CYS 40 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? 
disulf ? disulf3 A SG CYS 61 A CYS 97 1_555 A SG CYS 103 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? 
disulf ? disulf4 A SG CYS 245 A CYS 281 1_555 A SG CYS 269 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? 
disulf ? disulf5 B SG CYS 23 C CYS 23 1_555 B SG CYS 94 C CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? 
disulf ? disulf6 B SG CYS 140 C CYS 140 1_555 B SG CYS 200 C CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
disulf ? disulf7 C SG CYS 22 B CYS 22 1_555 C SG CYS 96 B CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? 
disulf ? disulf8 C SG CYS 143 B CYS 143 1_555 C SG CYS 199 B CYS 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? 
covale ? covale1 A ND2 ASN 45 A ASN 81 1_555 F C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? 
covale ? covale2 A ND2 ASN 129 A ASN 165 1_555 E C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? 
covale ? covale3 A ND2 ASN 249 A ASN 285 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
covale ? covale4 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? 
covale ? covale5 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 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 334 n n 
C1 O1 NAG sing 335 n n 
C1 O5 NAG sing 336 n n 
C1 H1 NAG sing 337 n n 
C2 C3 NAG sing 338 n n 
C2 N2 NAG sing 339 n n 
C2 H2 NAG sing 340 n n 
C3 C4 NAG sing 341 n n 
C3 O3 NAG sing 342 n n 
C3 H3 NAG sing 343 n n 
C4 C5 NAG sing 344 n n 
C4 O4 NAG sing 345 n n 
C4 H4 NAG sing 346 n n 
C5 C6 NAG sing 347 n n 
C5 O5 NAG sing 348 n n 
C5 H5 NAG sing 349 n n 
C6 O6 NAG sing 350 n n 
C6 H61 NAG sing 351 n n 
C6 H62 NAG sing 352 n n 
C7 C8 NAG sing 353 n n 
C7 N2 NAG sing 354 n n 
C7 O7 NAG doub 355 n n 
C8 H81 NAG sing 356 n n 
C8 H82 NAG sing 357 n n 
C8 H83 NAG sing 358 n n 
N2 HN2 NAG sing 359 n n 
O1 HO1 NAG sing 360 n n 
O3 HO3 NAG sing 361 n n 
O4 HO4 NAG sing 362 n n 
O6 HO6 NAG sing 363 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                     6XPX 
_atom_sites.fract_transf_matrix[1][1]    0.014616 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.004753 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009846 
_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]    0.013584 
_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
E 5 NAG A 1 401 312 NAG NAG . 
F 5 NAG A 1 402 313 NAG NAG . 
G 6 BCN A 1 403 401 BCN BCN . 
H 7 GOL A 1 404 501 GOL GOL . 
I 7 GOL A 1 405 601 GOL GOL . 
J 6 BCN A 1 406 701 BCN BCN . 
K 7 GOL A 1 407 801 GOL GOL . 
L 8 1PE C 1 301 301 1PE 1PE . 
M 7 GOL C 1 302 401 GOL GOL . 
N 7 GOL C 1 303 601 GOL GOL . 
O 7 GOL C 1 304 701 GOL GOL . 
P 7 GOL B 1 501 501 GOL GOL . 
Q 9 HOH A 1 501 3 HOH HOH . 
Q 9 HOH A 2 502 2 HOH HOH . 
Q 9 HOH A 3 503 13 HOH HOH . 
Q 9 HOH A 4 504 4 HOH HOH . 
Q 9 HOH A 5 505 8 HOH HOH . 
Q 9 HOH A 6 506 9 HOH HOH . 
Q 9 HOH A 7 507 12 HOH HOH . 
R 9 HOH C 1 401 5 HOH HOH . 
R 9 HOH C 2 402 11 HOH HOH . 
R 9 HOH C 3 403 10 HOH HOH . 
R 9 HOH C 4 404 6 HOH HOH . 
R 9 HOH C 5 405 16 HOH HOH . 
R 9 HOH C 6 406 1 HOH HOH . 
R 9 HOH C 7 407 15 HOH HOH . 
S 9 HOH B 1 601 14 HOH HOH . 
S 9 HOH B 2 602 7 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 . . . F 5 -16.392 2.369 -5.256 1 100.28 ? C1 NAG 402 A 1 
HETATM 2 C C2 NAG . . . F 5 -17.529 1.887 -4.346 1 111.1 ? C2 NAG 402 A 1 
HETATM 3 C C3 NAG . . . F 5 -18.877 2.38 -4.891 1 113.5 ? C3 NAG 402 A 1 
HETATM 4 C C4 NAG . . . F 5 -18.869 3.899 -5.006 1 114.73 ? C4 NAG 402 A 1 
HETATM 5 C C5 NAG . . . F 5 -17.727 4.34 -5.92 1 112.17 ? C5 NAG 402 A 1 
HETATM 6 C C6 NAG . . . F 5 -17.593 5.853 -6.045 1 113.99 ? C6 NAG 402 A 1 
HETATM 7 C C7 NAG . . . F 5 -16.911 -0.234 -3.208 1 119.5 ? C7 NAG 402 A 1 
HETATM 8 C C8 NAG . . . F 5 -17.031 -1.731 -3.249 1 116.66 ? C8 NAG 402 A 1 
HETATM 9 N N2 NAG . . . F 5 -17.522 0.433 -4.205 1 118.46 ? N2 NAG 402 A 1 
HETATM 10 O O3 NAG . . . F 5 -19.956 1.944 -4.069 1 115.25 ? O3 NAG 402 A 1 
HETATM 11 O O4 NAG . . . F 5 -20.122 4.38 -5.483 1 117.34 ? O4 NAG 402 A 1 
HETATM 12 O O5 NAG . . . F 5 -16.475 3.835 -5.418 1 108.5 ? O5 NAG 402 A 1 
HETATM 13 O O6 NAG . . . F 5 -17.06 6.498 -4.892 1 113.79 ? O6 NAG 402 A 1 
HETATM 14 O O7 NAG . . . F 5 -16.284 0.347 -2.313 1 121.38 ? O7 NAG 402 A 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    29 
_model_server_stats.query_time_ms           310 
_model_server_stats.encode_time_ms          12 
_model_server_stats.element_count           14 
#