data_4RFN
#
_model_server_result.job_id            WiUhcFU-cf5gsnA0hV332w 
_model_server_result.datetime_utc      '2024-10-12 12:25:34' 
_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          4rfn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"P","auth_seq_id":508}' 
#
_entry.id    4RFN 
#
_exptl.entry_id    4RFN 
_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    18 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          114.26 
_cell.angle_gamma         90 
_cell.entry_id            4RFN 
_cell.length_a            110.255 
_cell.length_b            77.827 
_cell.length_c            127.587 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4RFN 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        3 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 2 1' 
#
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,C,D,I,J,K,L,M,N,O,P,Q 1 1 
E,F,G,H,R,S,T,U,V,W,X,Y,Z 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
? 5 I N N 
? 5 J N N 
? 5 K N N 
? 5 L N N 
? 5 M N N 
? 5 N N N 
? 5 O N N 
? 5 P N N 
? 5 Q N N 
? 5 R N N 
? 5 S N N 
? 5 T N N 
? 5 U N N 
? 5 V N N 
? 5 W N N 
? 5 X N N 
? 5 Y N N 
? 5 Z 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 11 G CYS 54 1_555 A SG CYS 31 G CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf2 A SG CYS 76 G CYS 119 1_555 A SG CYS 89 G CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf3 A SG CYS 102 G CYS 218 1_555 A SG CYS 131 G CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf4 A SG CYS 112 G CYS 228 1_555 A SG CYS 123 G CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf5 A SG CYS 180 G CYS 296 1_555 A SG CYS 199 G CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf6 A SG CYS 245 G CYS 378 1_555 A SG CYS 306 G CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf7 A SG CYS 252 G CYS 385 1_555 A SG CYS 279 G CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf8 A SG CYS 262 G CYS 395 1_555 A SG CYS 271 G CYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
disulf ? disulf9 B SG CYS 24 H CYS 22 1_555 B SG CYS 98 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf10 B SG CYS 152 H CYS 140 1_555 B SG CYS 208 H CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf11 C SG CYS 22 L CYS 23 1_555 C SG CYS 89 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf12 C SG CYS 138 L CYS 134 1_555 C SG CYS 197 L CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf13 D SG CYS 6 M CYS 6 1_555 D SG CYS 24 M CYS 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf14 D SG CYS 10 M CYS 10 1_555 D SG CYS 26 M CYS 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf15 E SG CYS 11 A CYS 54 1_555 E SG CYS 31 A CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf16 E SG CYS 76 A CYS 119 1_555 E SG CYS 89 A CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf17 E SG CYS 102 A CYS 218 1_555 E SG CYS 131 A CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
disulf ? disulf18 E SG CYS 112 A CYS 228 1_555 E SG CYS 123 A CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
disulf ? disulf19 E SG CYS 180 A CYS 296 1_555 E SG CYS 199 A CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf20 E SG CYS 245 A CYS 378 1_555 E SG CYS 306 A CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf21 E SG CYS 252 A CYS 385 1_555 E SG CYS 279 A CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf22 E SG CYS 262 A CYS 395 1_555 E SG CYS 271 A CYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
disulf ? disulf23 F SG CYS 24 B CYS 22 1_555 F SG CYS 98 B CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf24 F SG CYS 152 B CYS 140 1_555 F SG CYS 208 B CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
disulf ? disulf25 G SG CYS 22 C CYS 23 1_555 G SG CYS 89 C CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf26 G SG CYS 138 C CYS 134 1_555 G SG CYS 197 C CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf27 H SG CYS 6 D CYS 6 1_555 H SG CYS 24 D CYS 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf28 H SG CYS 10 D CYS 10 1_555 H SG CYS 26 D CYS 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
covale ? covale1 A ND2 ASN 118 G ASN 234 1_555 I C1 NAG . G NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.295 ? 
covale ? covale2 A ND2 ASN 125 G ASN 241 1_555 J C1 NAG . G NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale3 A ND2 ASN 146 G ASN 262 1_555 K C1 NAG . G NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.297 ? 
covale ? covale4 A ND2 ASN 160 G ASN 276 1_555 L C1 NAG . G NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.298 ? 
covale ? covale5 A ND2 ASN 173 G ASN 289 1_555 M C1 NAG . G NAG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.303 ? 
covale ? covale6 A ND2 ASN 179 G ASN 295 1_555 N C1 NAG . G NAG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.285 ? 
covale ? covale7 A ND2 ASN 202 G ASN 334 1_555 O C1 NAG . G NAG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.295 ? 
covale ? covale8 A ND2 ASN 253 G ASN 386 1_555 P C1 NAG . G NAG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale9 A ND2 ASN 259 G ASN 392 1_555 Q C1 NAG . G NAG 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.369 ? 
covale ? covale10 D C MPT 1 M MPT 1 1_555 D N ASN 2 M ASN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.306 ? 
covale ? covale11 D C ALA 20 M ALA 20 1_555 D N DPR 21 M DPR 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? 
covale ? covale12 D C DPR 21 M DPR 21 1_555 D N THR 22 M THR 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale13 D C VAL 27 M VAL 27 1_555 D N NH2 28 M NH2 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.277 ? 
covale ? covale14 E ND2 ASN 118 A ASN 234 1_555 R C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.296 ? 
covale ? covale15 E ND2 ASN 125 A ASN 241 1_555 S C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.252 ? 
covale ? covale16 E ND2 ASN 146 A ASN 262 1_555 T C1 NAG . A NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.3 ? 
covale ? covale17 E ND2 ASN 160 A ASN 276 1_555 U C1 NAG . A NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? 
covale ? covale18 E ND2 ASN 173 A ASN 289 1_555 V C1 NAG . A NAG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.297 ? 
covale ? covale19 E ND2 ASN 179 A ASN 295 1_555 W C1 NAG . A NAG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.294 ? 
covale ? covale20 E ND2 ASN 202 A ASN 334 1_555 X C1 NAG . A NAG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.3 ? 
covale ? covale21 E ND2 ASN 253 A ASN 386 1_555 Y C1 NAG . A NAG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? 
covale ? covale22 E ND2 ASN 259 A ASN 392 1_555 Z C1 NAG . A NAG 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.381 ? 
covale ? covale23 H C MPT 1 D MPT 1 1_555 H N ASN 2 D ASN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.285 ? 
covale ? covale24 H C ALA 20 D ALA 20 1_555 H N DPR 21 D DPR 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? 
covale ? covale25 H C DPR 21 D DPR 21 1_555 H N THR 22 D THR 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale26 H C VAL 27 D VAL 27 1_555 H N NH2 28 D NH2 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.276 ? 
#
_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 263 n n 
C1 O1 NAG sing 264 n n 
C1 O5 NAG sing 265 n n 
C1 H1 NAG sing 266 n n 
C2 C3 NAG sing 267 n n 
C2 N2 NAG sing 268 n n 
C2 H2 NAG sing 269 n n 
C3 C4 NAG sing 270 n n 
C3 O3 NAG sing 271 n n 
C3 H3 NAG sing 272 n n 
C4 C5 NAG sing 273 n n 
C4 O4 NAG sing 274 n n 
C4 H4 NAG sing 275 n n 
C5 C6 NAG sing 276 n n 
C5 O5 NAG sing 277 n n 
C5 H5 NAG sing 278 n n 
C6 O6 NAG sing 279 n n 
C6 H61 NAG sing 280 n n 
C6 H62 NAG sing 281 n n 
C7 C8 NAG sing 282 n n 
C7 N2 NAG sing 283 n n 
C7 O7 NAG doub 284 n n 
C8 H81 NAG sing 285 n n 
C8 H82 NAG sing 286 n n 
C8 H83 NAG sing 287 n n 
N2 HN2 NAG sing 288 n n 
O1 HO1 NAG sing 289 n n 
O3 HO3 NAG sing 290 n n 
O4 HO4 NAG sing 291 n n 
O6 HO6 NAG sing 292 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                     4RFN 
_atom_sites.fract_transf_matrix[1][1]    0.00907 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.004088 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012849 
_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]    0.008597 
_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 5 NAG G 1 501 501 NAG NAG . 
J 5 NAG G 1 502 502 NAG NAG . 
K 5 NAG G 1 503 504 NAG NAG . 
L 5 NAG G 1 504 505 NAG NAG . 
M 5 NAG G 1 505 506 NAG NAG . 
N 5 NAG G 1 506 507 NAG NAG . 
O 5 NAG G 1 507 508 NAG NAG . 
P 5 NAG G 1 508 509 NAG NAG . 
Q 5 NAG G 1 509 510 NAG NAG . 
R 5 NAG A 1 501 501 NAG NAG . 
S 5 NAG A 1 502 502 NAG NAG . 
T 5 NAG A 1 503 504 NAG NAG . 
U 5 NAG A 1 504 505 NAG NAG . 
V 5 NAG A 1 505 506 NAG NAG . 
W 5 NAG A 1 506 507 NAG NAG . 
X 5 NAG A 1 507 508 NAG NAG . 
Y 5 NAG A 1 508 509 NAG NAG . 
Z 5 NAG A 1 509 510 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 . . . P 5 5.846 -17.266 36.818 1 121.71 ? C1 NAG 508 G 1 
HETATM 2 C C2 NAG . . . P 5 5.016 -15.97 36.93 1 131.28 ? C2 NAG 508 G 1 
HETATM 3 C C3 NAG . . . P 5 4.63 -15.495 38.329 1 132.63 ? C3 NAG 508 G 1 
HETATM 4 C C4 NAG . . . P 5 4.283 -16.671 39.223 1 137.35 ? C4 NAG 508 G 1 
HETATM 5 C C5 NAG . . . P 5 5.479 -17.607 39.241 1 139.06 ? C5 NAG 508 G 1 
HETATM 6 C C6 NAG . . . P 5 5.321 -18.785 40.188 1 139.87 ? C6 NAG 508 G 1 
HETATM 7 C C7 NAG . . . P 5 5.257 -14.375 35.089 1 139.32 ? C7 NAG 508 G 1 
HETATM 8 C C8 NAG . . . P 5 6.003 -13.195 34.539 1 141.69 ? C8 NAG 508 G 1 
HETATM 9 N N2 NAG . . . P 5 5.654 -14.831 36.277 1 132.21 ? N2 NAG 508 G 1 
HETATM 10 O O3 NAG . . . P 5 3.536 -14.638 38.122 1 127.28 ? O3 NAG 508 G 1 
HETATM 11 O O4 NAG . . . P 5 4.029 -16.198 40.511 1 141.04 ? O4 NAG 508 G 1 
HETATM 12 O O5 NAG . . . P 5 5.516 -18.13 37.93 1 139.28 ? O5 NAG 508 G 1 
HETATM 13 O O6 NAG . . . P 5 4.11 -19.425 39.865 1 140.42 ? O6 NAG 508 G 1 
HETATM 14 O O7 NAG . . . P 5 4.336 -14.875 34.439 1 142.83 ? O7 NAG 508 G 1 
#
_model_server_stats.io_time_ms              28 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           278 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           14 
#