data_4PBV
#
_model_server_result.job_id            63SiwhygOOAV9wk3pKmWiQ 
_model_server_result.datetime_utc      '2024-12-22 06:23:26' 
_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          4pbv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":403}' 
#
_entry.id    4PBV 
#
_exptl.entry_id    4PBV 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-acetamido-2-deoxy-beta-D-glucopyranose 
_entity.pdbx_number_of_molecules    5 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          109.79 
_cell.angle_gamma         90 
_cell.entry_id            4PBV 
_cell.length_a            68.3 
_cell.length_b            122.16 
_cell.length_c            98.61 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4PBV 
_symmetry.cell_setting             . 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1 21 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 Dimeric 2 software_defined_assembly 1 
PISA Dimeric 2 software_defined_assembly 2 
PISA Monomeric 1 software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,F,G,H,M,O 1 1 
B,D,I,J,K,N,P 2 1 
E,L,Q 3 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 F N N 
? 3 G N N 
? 3 H N N 
? 3 I N N 
? 3 J 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 4 A CYS 32 1_555 A SG CYS 10 A CYS 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
disulf ? disulf2 A SG CYS 8 A CYS 36 1_555 A SG CYS 17 A CYS 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? 
disulf ? disulf3 A SG CYS 121 A CYS 164 1_555 A SG CYS 146 A CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? 
disulf ? disulf4 A SG CYS 123 A CYS 166 1_555 A SG CYS 164 A CYS 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? 
disulf ? disulf5 A SG CYS 188 A CYS 231 1_555 A SG CYS 241 A CYS 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf6 B SG CYS 4 B CYS 32 1_555 B SG CYS 10 B CYS 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? 
disulf ? disulf7 B SG CYS 8 B CYS 36 1_555 B SG CYS 17 B CYS 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
disulf ? disulf8 B SG CYS 121 B CYS 164 1_555 B SG CYS 146 B CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? 
disulf ? disulf9 B SG CYS 123 B CYS 166 1_555 B SG CYS 164 B CYS 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? 
disulf ? disulf10 B SG CYS 188 B CYS 231 1_555 B SG CYS 241 B CYS 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? 
disulf ? disulf11 C SG CYS 28 C CYS 53 1_555 C SG CYS 81 C CYS 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf12 C SG CYS 130 C CYS 155 1_555 C SG CYS 181 C CYS 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
disulf ? disulf13 D SG CYS 28 D CYS 53 1_555 D SG CYS 81 D CYS 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? 
disulf ? disulf14 D SG CYS 130 D CYS 155 1_555 D SG CYS 181 D CYS 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? 
disulf ? disulf15 E SG CYS 28 E CYS 53 1_555 E SG CYS 81 E CYS 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? 
disulf ? disulf16 E SG CYS 130 E CYS 155 1_555 E SG CYS 181 E CYS 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
covale ? covale1 A ND2 ASN 36 A ASN 79 1_555 F C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? 
covale ? covale2 A ND2 ASN 160 A ASN 203 1_555 H C1 NAG . A NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? 
covale ? covale3 A ND2 ASN 229 A ASN 272 1_555 G C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? 
covale ? covale4 B ND2 ASN 36 B ASN 79 1_555 I C1 NAG . B NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? 
covale ? covale5 B ND2 ASN 229 B ASN 272 1_555 J C1 NAG . B NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? 
#
_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 237 n n 
C1 O1 NAG sing 238 n n 
C1 O5 NAG sing 239 n n 
C1 H1 NAG sing 240 n n 
C2 C3 NAG sing 241 n n 
C2 N2 NAG sing 242 n n 
C2 H2 NAG sing 243 n n 
C3 C4 NAG sing 244 n n 
C3 O3 NAG sing 245 n n 
C3 H3 NAG sing 246 n n 
C4 C5 NAG sing 247 n n 
C4 O4 NAG sing 248 n n 
C4 H4 NAG sing 249 n n 
C5 C6 NAG sing 250 n n 
C5 O5 NAG sing 251 n n 
C5 H5 NAG sing 252 n n 
C6 O6 NAG sing 253 n n 
C6 H61 NAG sing 254 n n 
C6 H62 NAG sing 255 n n 
C7 C8 NAG sing 256 n n 
C7 N2 NAG sing 257 n n 
C7 O7 NAG doub 258 n n 
C8 H81 NAG sing 259 n n 
C8 H82 NAG sing 260 n n 
C8 H83 NAG sing 261 n n 
N2 HN2 NAG sing 262 n n 
O1 HO1 NAG sing 263 n n 
O3 HO3 NAG sing 264 n n 
O4 HO4 NAG sing 265 n n 
O6 HO6 NAG sing 266 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                     4PBV 
_atom_sites.fract_transf_matrix[1][1]    0.014641 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.005268 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008186 
_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]    0.010777 
_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
F 3 NAG A 1 401 1 NAG NAG . 
G 3 NAG A 1 402 3 NAG NAG . 
H 3 NAG A 1 403 4 NAG NAG . 
I 3 NAG B 1 401 2 NAG NAG . 
J 3 NAG B 1 402 5 NAG NAG . 
K 4 SO4 D 1 401 1 SO4 SO4 . 
L 4 SO4 E 1 401 2 SO4 SO4 . 
M 5 HOH A 1 501 14 HOH HOH . 
M 5 HOH A 2 502 83 HOH HOH . 
M 5 HOH A 3 503 189 HOH HOH . 
M 5 HOH A 4 504 17 HOH HOH . 
M 5 HOH A 5 505 180 HOH HOH . 
M 5 HOH A 6 506 81 HOH HOH . 
M 5 HOH A 7 507 175 HOH HOH . 
M 5 HOH A 8 508 3 HOH HOH . 
M 5 HOH A 9 509 160 HOH HOH . 
M 5 HOH A 10 510 13 HOH HOH . 
M 5 HOH A 11 511 174 HOH HOH . 
M 5 HOH A 12 512 114 HOH HOH . 
M 5 HOH A 13 513 26 HOH HOH . 
M 5 HOH A 14 514 15 HOH HOH . 
M 5 HOH A 15 515 84 HOH HOH . 
M 5 HOH A 16 516 120 HOH HOH . 
M 5 HOH A 17 517 24 HOH HOH . 
M 5 HOH A 18 518 196 HOH HOH . 
M 5 HOH A 19 519 181 HOH HOH . 
M 5 HOH A 20 520 18 HOH HOH . 
M 5 HOH A 21 521 82 HOH HOH . 
M 5 HOH A 22 522 137 HOH HOH . 
M 5 HOH A 23 523 128 HOH HOH . 
M 5 HOH A 24 524 177 HOH HOH . 
N 5 HOH B 1 501 33 HOH HOH . 
N 5 HOH B 2 502 35 HOH HOH . 
N 5 HOH B 3 503 38 HOH HOH . 
N 5 HOH B 4 504 195 HOH HOH . 
N 5 HOH B 5 505 11 HOH HOH . 
N 5 HOH B 6 506 87 HOH HOH . 
N 5 HOH B 7 507 102 HOH HOH . 
N 5 HOH B 8 508 27 HOH HOH . 
N 5 HOH B 9 509 143 HOH HOH . 
N 5 HOH B 10 510 16 HOH HOH . 
N 5 HOH B 11 511 31 HOH HOH . 
N 5 HOH B 12 512 85 HOH HOH . 
N 5 HOH B 13 513 187 HOH HOH . 
N 5 HOH B 14 514 12 HOH HOH . 
N 5 HOH B 15 515 88 HOH HOH . 
N 5 HOH B 16 516 30 HOH HOH . 
N 5 HOH B 17 517 7 HOH HOH . 
N 5 HOH B 18 518 28 HOH HOH . 
N 5 HOH B 19 519 36 HOH HOH . 
N 5 HOH B 20 520 149 HOH HOH . 
N 5 HOH B 21 521 192 HOH HOH . 
N 5 HOH B 22 522 21 HOH HOH . 
N 5 HOH B 23 523 20 HOH HOH . 
N 5 HOH B 24 524 176 HOH HOH . 
O 5 HOH C 1 401 146 HOH HOH . 
O 5 HOH C 2 402 59 HOH HOH . 
O 5 HOH C 3 403 50 HOH HOH . 
O 5 HOH C 4 404 103 HOH HOH . 
O 5 HOH C 5 405 161 HOH HOH . 
O 5 HOH C 6 406 104 HOH HOH . 
O 5 HOH C 7 407 76 HOH HOH . 
O 5 HOH C 8 408 42 HOH HOH . 
O 5 HOH C 9 409 43 HOH HOH . 
O 5 HOH C 10 410 44 HOH HOH . 
O 5 HOH C 11 411 165 HOH HOH . 
O 5 HOH C 12 412 162 HOH HOH . 
O 5 HOH C 13 413 178 HOH HOH . 
O 5 HOH C 14 414 46 HOH HOH . 
O 5 HOH C 15 415 58 HOH HOH . 
O 5 HOH C 16 416 123 HOH HOH . 
O 5 HOH C 17 417 124 HOH HOH . 
P 5 HOH D 1 501 191 HOH HOH . 
P 5 HOH D 2 502 72 HOH HOH . 
P 5 HOH D 3 503 8 HOH HOH . 
P 5 HOH D 4 504 153 HOH HOH . 
P 5 HOH D 5 505 144 HOH HOH . 
P 5 HOH D 6 506 73 HOH HOH . 
P 5 HOH D 7 507 48 HOH HOH . 
P 5 HOH D 8 508 171 HOH HOH . 
P 5 HOH D 9 509 198 HOH HOH . 
P 5 HOH D 10 510 172 HOH HOH . 
P 5 HOH D 11 511 55 HOH HOH . 
P 5 HOH D 12 512 173 HOH HOH . 
P 5 HOH D 13 513 91 HOH HOH . 
P 5 HOH D 14 514 77 HOH HOH . 
P 5 HOH D 15 515 60 HOH HOH . 
P 5 HOH D 16 516 57 HOH HOH . 
P 5 HOH D 17 517 75 HOH HOH . 
P 5 HOH D 18 518 41 HOH HOH . 
P 5 HOH D 19 519 108 HOH HOH . 
P 5 HOH D 20 520 51 HOH HOH . 
P 5 HOH D 21 521 98 HOH HOH . 
P 5 HOH D 22 522 90 HOH HOH . 
P 5 HOH D 23 523 110 HOH HOH . 
P 5 HOH D 24 524 52 HOH HOH . 
P 5 HOH D 25 525 194 HOH HOH . 
P 5 HOH D 26 526 139 HOH HOH . 
P 5 HOH D 27 527 106 HOH HOH . 
P 5 HOH D 28 528 197 HOH HOH . 
P 5 HOH D 29 529 67 HOH HOH . 
P 5 HOH D 30 530 107 HOH HOH . 
P 5 HOH D 31 531 63 HOH HOH . 
P 5 HOH D 32 532 9 HOH HOH . 
P 5 HOH D 33 533 170 HOH HOH . 
P 5 HOH D 34 534 154 HOH HOH . 
P 5 HOH D 35 535 61 HOH HOH . 
P 5 HOH D 36 536 6 HOH HOH . 
P 5 HOH D 37 537 141 HOH HOH . 
P 5 HOH D 38 538 167 HOH HOH . 
P 5 HOH D 39 539 190 HOH HOH . 
P 5 HOH D 40 540 45 HOH HOH . 
P 5 HOH D 41 541 179 HOH HOH . 
P 5 HOH D 42 542 166 HOH HOH . 
Q 5 HOH E 1 501 49 HOH HOH . 
Q 5 HOH E 2 502 184 HOH HOH . 
Q 5 HOH E 3 503 155 HOH HOH . 
Q 5 HOH E 4 504 131 HOH HOH . 
Q 5 HOH E 5 505 185 HOH HOH . 
Q 5 HOH E 6 506 1 HOH HOH . 
Q 5 HOH E 7 507 193 HOH HOH . 
Q 5 HOH E 8 508 5 HOH HOH . 
Q 5 HOH E 9 509 69 HOH HOH . 
Q 5 HOH E 10 510 70 HOH HOH . 
Q 5 HOH E 11 511 156 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 . . . H 3 -7.632 -5.01 -78.372 1 89.68 ? C1 NAG 403 A 1 
HETATM 2 C C2 NAG . . . H 3 -6.243 -5.623 -78.227 1 94.02 ? C2 NAG 403 A 1 
HETATM 3 C C3 NAG . . . H 3 -5.271 -4.805 -79.077 1 95.37 ? C3 NAG 403 A 1 
HETATM 4 C C4 NAG . . . H 3 -5.803 -4.547 -80.496 1 98.46 ? C4 NAG 403 A 1 
HETATM 5 C C5 NAG . . . H 3 -7.332 -4.439 -80.631 1 97.78 ? C5 NAG 403 A 1 
HETATM 6 C C6 NAG . . . H 3 -7.779 -4.753 -82.056 1 94.52 ? C6 NAG 403 A 1 
HETATM 7 C C7 NAG . . . H 3 -6.407 -6.556 -75.972 1 94.85 ? C7 NAG 403 A 1 
HETATM 8 C C8 NAG . . . H 3 -5.936 -6.536 -74.541 1 93.83 ? C8 NAG 403 A 1 
HETATM 9 N N2 NAG . . . H 3 -5.853 -5.68 -76.824 1 92.72 ? N2 NAG 403 A 1 
HETATM 10 O O3 NAG . . . H 3 -4.026 -5.463 -79.166 1 92.83 ? O3 NAG 403 A 1 
HETATM 11 O O4 NAG . . . H 3 -5.248 -3.336 -80.962 1 103 ? O4 NAG 403 A 1 
HETATM 12 O O5 NAG . . . H 3 -8.036 -5.262 -79.708 1 96.81 ? O5 NAG 403 A 1 
HETATM 13 O O6 NAG . . . H 3 -9.148 -4.438 -82.16 1 94.17 ? O6 NAG 403 A 1 
HETATM 14 O O7 NAG . . . H 3 -7.275 -7.367 -76.308 1 90.83 ? O7 NAG 403 A 1 
#
_model_server_stats.io_time_ms              20 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           225 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           14 
#