data_3KBH
#
_model_server_result.job_id            17pw689iYO0Nu9l7ApzVFg 
_model_server_result.datetime_utc      '2024-11-27 23:48:08' 
_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          3kbh 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"O","auth_seq_id":1486}' 
#
_entry.id    3KBH 
#
_exptl.entry_id    3KBH 
_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    16 
_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            3KBH 
_cell.length_a            77.764 
_cell.length_b            77.764 
_cell.length_c            631.095 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3KBH 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        78 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA tetrameric 4 author_and_software_defined_assembly 1 
PISA tetrameric 4 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,E,F,I,J,K,L,Q,R,S,T 1 1 
C,D,G,H,M,N,O,P,U,V,W,X 2 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 I N N 
? 3 J N N 
? 3 K N N 
? 3 L N N 
? 3 M N N 
? 3 N N N 
? 3 O N N 
? 3 P N N 
? 3 Q N N 
? 3 R N N 
? 3 S N N 
? 3 T N N 
? 3 U N N 
? 3 V N N 
? 3 W N N 
? 3 X 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 115 A CYS 133 1_555 A SG CYS 123 A CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? 
disulf ? disulf2 A SG CYS 326 A CYS 344 1_555 A SG CYS 343 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf3 A SG CYS 512 A CYS 530 1_555 A SG CYS 524 A CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
disulf ? disulf4 B SG CYS 17 E CYS 497 1_555 B SG CYS 20 E CYS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
disulf ? disulf5 B SG CYS 36 E CYS 516 1_555 B SG CYS 87 E CYS 567 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? 
disulf ? disulf6 B SG CYS 70 E CYS 550 1_555 B SG CYS 97 E CYS 577 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? 
disulf ? disulf7 C SG CYS 115 B CYS 133 1_555 C SG CYS 123 B CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? 
disulf ? disulf8 C SG CYS 326 B CYS 344 1_555 C SG CYS 343 B CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
disulf ? disulf9 C SG CYS 512 B CYS 530 1_555 C SG CYS 524 B CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
disulf ? disulf10 D SG CYS 17 F CYS 497 1_555 D SG CYS 20 F CYS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? 
disulf ? disulf11 D SG CYS 36 F CYS 516 1_555 D SG CYS 87 F CYS 567 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
disulf ? disulf12 D SG CYS 70 F CYS 550 1_555 D SG CYS 97 F CYS 577 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? 
disulf ? disulf13 E SG CYS 115 C CYS 133 1_555 E SG CYS 123 C CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? 
disulf ? disulf14 E SG CYS 326 C CYS 344 1_555 E SG CYS 343 C CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? 
disulf ? disulf15 E SG CYS 512 C CYS 530 1_555 E SG CYS 524 C CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf16 F SG CYS 17 G CYS 497 1_555 F SG CYS 20 G CYS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? 
disulf ? disulf17 F SG CYS 36 G CYS 516 1_555 F SG CYS 87 G CYS 567 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf18 F SG CYS 70 G CYS 550 1_555 F SG CYS 97 G CYS 577 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? 
disulf ? disulf19 G SG CYS 115 D CYS 133 1_555 G SG CYS 123 D CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? 
disulf ? disulf20 G SG CYS 326 D CYS 344 1_555 G SG CYS 343 D CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf21 G SG CYS 512 D CYS 530 1_555 G SG CYS 524 D CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
disulf ? disulf22 H SG CYS 17 H CYS 497 1_555 H SG CYS 20 H CYS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? 
disulf ? disulf23 H SG CYS 36 H CYS 516 1_555 H SG CYS 87 H CYS 567 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf24 H SG CYS 70 H CYS 550 1_555 H SG CYS 97 H CYS 577 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? 
covale ? covale1 A ND2 ASN 72 A ASN 90 1_555 I C1 NAG . A NAG 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? 
covale ? covale2 A ND2 ASN 528 A ASN 546 1_555 J C1 NAG . A NAG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.474 ? 
covale ? covale3 B ND2 ASN 6 E ASN 486 1_555 K C1 NAG . E NAG 1486 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? 
covale ? covale4 B ND2 ASN 32 E ASN 512 1_555 L C1 NAG . E NAG 1512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.478 ? 
covale ? covale5 C ND2 ASN 72 B ASN 90 1_555 M C1 NAG . B NAG 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? 
covale ? covale6 C ND2 ASN 528 B ASN 546 1_555 N C1 NAG . B NAG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.478 ? 
covale ? covale7 D ND2 ASN 6 F ASN 486 1_555 O C1 NAG . F NAG 1486 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? 
covale ? covale8 D ND2 ASN 32 F ASN 512 1_555 P C1 NAG . F NAG 1512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.486 ? 
covale ? covale9 E ND2 ASN 72 C ASN 90 1_555 Q C1 NAG . C NAG 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? 
covale ? covale10 E ND2 ASN 528 C ASN 546 1_555 R C1 NAG . C NAG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.48 ? 
covale ? covale11 F ND2 ASN 6 G ASN 486 1_555 S C1 NAG . G NAG 1486 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? 
covale ? covale12 F ND2 ASN 32 G ASN 512 1_555 T C1 NAG . G NAG 1512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.486 ? 
covale ? covale13 G ND2 ASN 72 D ASN 90 1_555 U C1 NAG . D NAG 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? 
covale ? covale14 G ND2 ASN 528 D ASN 546 1_555 V C1 NAG . D NAG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.474 ? 
covale ? covale15 H ND2 ASN 6 H ASN 486 1_555 W C1 NAG . H NAG 1486 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? 
covale ? covale16 H ND2 ASN 32 H ASN 512 1_555 X C1 NAG . H NAG 1512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.482 ? 
#
_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 235 n n 
C1 O1 NAG sing 236 n n 
C1 O5 NAG sing 237 n n 
C1 H1 NAG sing 238 n n 
C2 C3 NAG sing 239 n n 
C2 N2 NAG sing 240 n n 
C2 H2 NAG sing 241 n n 
C3 C4 NAG sing 242 n n 
C3 O3 NAG sing 243 n n 
C3 H3 NAG sing 244 n n 
C4 C5 NAG sing 245 n n 
C4 O4 NAG sing 246 n n 
C4 H4 NAG sing 247 n n 
C5 C6 NAG sing 248 n n 
C5 O5 NAG sing 249 n n 
C5 H5 NAG sing 250 n n 
C6 O6 NAG sing 251 n n 
C6 H61 NAG sing 252 n n 
C6 H62 NAG sing 253 n n 
C7 C8 NAG sing 254 n n 
C7 N2 NAG sing 255 n n 
C7 O7 NAG doub 256 n n 
C8 H81 NAG sing 257 n n 
C8 H82 NAG sing 258 n n 
C8 H83 NAG sing 259 n n 
N2 HN2 NAG sing 260 n n 
O1 HO1 NAG sing 261 n n 
O3 HO3 NAG sing 262 n n 
O4 HO4 NAG sing 263 n n 
O6 HO6 NAG sing 264 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                     3KBH 
_atom_sites.fract_transf_matrix[1][1]    0.012859 
_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]    0.012859 
_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]    0.001585 
_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
I 3 NAG A 1 800 800 NAG NAG . 
J 3 NAG A 1 801 801 NAG NAG . 
K 3 NAG E 1 1486 1486 NAG NAG . 
L 3 NAG E 1 1512 1512 NAG NAG . 
M 3 NAG B 1 800 800 NAG NAG . 
N 3 NAG B 1 801 801 NAG NAG . 
O 3 NAG F 1 1486 1486 NAG NAG . 
P 3 NAG F 1 1512 1512 NAG NAG . 
Q 3 NAG C 1 800 800 NAG NAG . 
R 3 NAG C 1 801 801 NAG NAG . 
S 3 NAG G 1 1486 1486 NAG NAG . 
T 3 NAG G 1 1512 1512 NAG NAG . 
U 3 NAG D 1 800 800 NAG NAG . 
V 3 NAG D 1 801 801 NAG NAG . 
W 3 NAG H 1 1486 1486 NAG NAG . 
X 3 NAG H 1 1512 1512 NAG NAG . 
#
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 . . . O 3 -53.855 -50.501 70.276 1 86.23 ? C1 NAG 1486 F 1 
HETATM 2 C C2 NAG . . . O 3 -53.664 -51.87 70.947 1 101.78 ? C2 NAG 1486 F 1 
HETATM 3 C C3 NAG . . . O 3 -52.935 -52.863 70.036 1 103.51 ? C3 NAG 1486 F 1 
HETATM 4 C C4 NAG . . . O 3 -53.489 -52.826 68.613 1 104.28 ? C4 NAG 1486 F 1 
HETATM 5 C C5 NAG . . . O 3 -53.52 -51.386 68.108 1 102.32 ? C5 NAG 1486 F 1 
HETATM 6 C C6 NAG . . . O 3 -54.076 -51.239 66.702 1 104.19 ? C6 NAG 1486 F 1 
HETATM 7 C C7 NAG . . . O 3 -53.559 -51.625 73.386 1 107.9 ? C7 NAG 1486 F 1 
HETATM 8 C C8 NAG . . . O 3 -52.68 -51.492 74.594 1 108.36 ? C8 NAG 1486 F 1 
HETATM 9 N N2 NAG . . . O 3 -52.947 -51.735 72.206 1 105.06 ? N2 NAG 1486 F 1 
HETATM 10 O O3 NAG . . . O 3 -53.04 -54.175 70.547 1 104.9 ? O3 NAG 1486 F 1 
HETATM 11 O O4 NAG . . . O 3 -52.69 -53.635 67.785 1 105.71 ? O4 NAG 1486 F 1 
HETATM 12 O O5 NAG . . . O 3 -54.366 -50.67 68.968 1 95.07 ? O5 NAG 1486 F 1 
HETATM 13 O O6 NAG . . . O 3 -54.101 -49.866 66.391 1 104.69 ? O6 NAG 1486 F 1 
HETATM 14 O O7 NAG . . . O 3 -54.78 -51.624 73.521 1 109.07 ? O7 NAG 1486 F 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    27 
_model_server_stats.query_time_ms           282 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           14 
#