data_3PVM
#
_model_server_result.job_id            7t048YYaZcciRN0_9BHzyg 
_model_server_result.datetime_utc      '2024-10-18 16:23:17' 
_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          3pvm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":2003}' 
#
_entry.id    3PVM 
#
_exptl.entry_id    3PVM 
_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    6 
_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            3PVM 
_cell.length_a            176.52 
_cell.length_b            179.2 
_cell.length_c            389.69 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3PVM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        17 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 2 2 21' 
#
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 author_and_software_defined_assembly 1 
PISA dimeric 2 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,G 1 1 
C,D,H,I,J 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 E N N 
? 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 567 A CYS 567 1_555 A SG CYS 810 A CYS 810 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? 
disulf ? disulf2 A SG CYS 634 A CYS 634 1_555 A SG CYS 669 A CYS 669 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? 
disulf ? disulf3 A SG CYS 698 A CYS 698 1_555 A SG CYS 724 A CYS 724 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? 
disulf ? disulf4 A SG CYS 699 A CYS 699 1_555 A SG CYS 731 A CYS 731 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf5 A SG CYS 711 A CYS 711 1_555 A SG CYS 732 A CYS 732 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
disulf ? disulf6 A SG CYS 856 A CYS 856 1_555 A SG CYS 883 A CYS 883 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? 
disulf ? disulf7 A SG CYS 866 A CYS 866 1_555 A SG CYS 1527 A CYS 1527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf8 A SG CYS 1101 A CYS 1101 1_555 A SG CYS 1159 A CYS 1159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
disulf ? disulf9 A SG CYS 1375 A CYS 1375 1_555 A SG CYS 1505 A CYS 1505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? 
disulf ? disulf10 A SG CYS 1405 A CYS 1405 1_555 A SG CYS 1474 A CYS 1474 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? 
disulf ? disulf11 A SG CYS 1532 A CYS 1532 1_555 A SG CYS 1606 A CYS 1606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? 
disulf ? disulf12 A SG CYS 1553 A CYS 1553 1_555 A SG CYS 1676 A CYS 1676 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? 
disulf ? disulf13 A SG CYS 1654 A CYS 1654 1_555 A SG CYS 1657 A CYS 1657 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
disulf ? disulf14 B SG CYS 544 B CYS 544 1_555 B SG CYS 801 B CYS 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
disulf ? disulf15 B SG CYS 609 B CYS 609 1_555 B SG CYS 644 B CYS 644 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
disulf ? disulf16 B SG CYS 857 B CYS 857 1_555 B SG CYS 1492 B CYS 1492 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
disulf ? disulf17 B SG CYS 1340 B CYS 1340 1_555 B SG CYS 1468 B CYS 1468 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? 
disulf ? disulf18 B SG CYS 1368 B CYS 1368 1_555 B SG CYS 1437 B CYS 1437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? 
disulf ? disulf19 B SG CYS 1485 B CYS 1485 1_555 B SG CYS 1490 B CYS 1490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
disulf ? disulf20 B SG CYS 1497 B CYS 1497 1_555 B SG CYS 1569 B CYS 1569 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? 
disulf ? disulf21 B SG CYS 1516 B CYS 1516 1_555 B SG CYS 1640 B CYS 1640 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? 
disulf ? disulf22 B SG CYS 1616 B CYS 1616 1_555 B SG CYS 1625 B CYS 1625 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf23 C SG CYS 567 C CYS 567 1_555 C SG CYS 810 C CYS 810 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? 
disulf ? disulf24 C SG CYS 634 C CYS 634 1_555 C SG CYS 669 C CYS 669 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? 
disulf ? disulf25 C SG CYS 698 C CYS 698 1_555 C SG CYS 724 C CYS 724 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
disulf ? disulf26 C SG CYS 699 C CYS 699 1_555 C SG CYS 731 C CYS 731 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? 
disulf ? disulf27 C SG CYS 711 C CYS 711 1_555 C SG CYS 732 C CYS 732 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
disulf ? disulf28 C SG CYS 856 C CYS 856 1_555 C SG CYS 883 C CYS 883 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? 
disulf ? disulf29 C SG CYS 866 C CYS 866 1_555 C SG CYS 1527 C CYS 1527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf30 C SG CYS 1101 C CYS 1101 1_555 C SG CYS 1159 C CYS 1159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
disulf ? disulf31 C SG CYS 1375 C CYS 1375 1_555 C SG CYS 1505 C CYS 1505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? 
disulf ? disulf32 C SG CYS 1405 C CYS 1405 1_555 C SG CYS 1474 C CYS 1474 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
disulf ? disulf33 C SG CYS 1532 C CYS 1532 1_555 C SG CYS 1606 C CYS 1606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? 
disulf ? disulf34 C SG CYS 1553 C CYS 1553 1_555 C SG CYS 1676 C CYS 1676 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? 
disulf ? disulf35 C SG CYS 1654 C CYS 1654 1_555 C SG CYS 1657 C CYS 1657 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
disulf ? disulf36 D SG CYS 544 D CYS 544 1_555 D SG CYS 801 D CYS 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? 
disulf ? disulf37 D SG CYS 609 D CYS 609 1_555 D SG CYS 644 D CYS 644 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf38 D SG CYS 857 D CYS 857 1_555 D SG CYS 1492 D CYS 1492 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? 
disulf ? disulf39 D SG CYS 1340 D CYS 1340 1_555 D SG CYS 1468 D CYS 1468 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? 
disulf ? disulf40 D SG CYS 1368 D CYS 1368 1_555 D SG CYS 1437 D CYS 1437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? 
disulf ? disulf41 D SG CYS 1485 D CYS 1485 1_555 D SG CYS 1490 D CYS 1490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
disulf ? disulf42 D SG CYS 1497 D CYS 1497 1_555 D SG CYS 1569 D CYS 1569 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
disulf ? disulf43 D SG CYS 1516 D CYS 1516 1_555 D SG CYS 1640 D CYS 1640 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
disulf ? disulf44 D SG CYS 1616 D CYS 1616 1_555 D SG CYS 1625 D CYS 1625 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
covale ? covale1 A ND2 ASN 911 A ASN 911 1_555 E C1 NAG . A NAG 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.472 ? 
covale ? covale2 B ND2 ASN 209 B ASN 209 1_555 F C1 NAG . B NAG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.403 ? 
covale ? covale3 B ND2 ASN 1346 B ASN 1346 1_555 G C1 NAG . B NAG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.475 ? 
covale ? covale4 C ND2 ASN 911 C ASN 911 1_555 H C1 NAG . C NAG 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? 
covale ? covale5 D ND2 ASN 209 D ASN 209 1_555 I C1 NAG . D NAG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? 
covale ? covale6 D ND2 ASN 1346 D ASN 1346 1_555 J C1 NAG . D NAG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.475 ? 
#
_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                     3PVM 
_atom_sites.fract_transf_matrix[1][1]    0.005665 
_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]    0.00558 
_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]    0.002566 
_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 3 NAG A 1 2003 2003 NAG NAG . 
F 3 NAG B 1 2001 2001 NAG NAG . 
G 3 NAG B 1 2002 2002 NAG NAG . 
H 3 NAG C 1 2003 2003 NAG NAG . 
I 3 NAG D 1 2001 2001 NAG NAG . 
J 3 NAG D 1 2002 2002 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 . . . H 3 32.479 8.131 -90.843 1 271.68 ? C1 NAG 2003 C 1 
HETATM 2 C C2 NAG . . . H 3 33.446 6.953 -90.992 1 270.26 ? C2 NAG 2003 C 1 
HETATM 3 C C3 NAG . . . H 3 34.966 7.228 -90.901 1 272.46 ? C3 NAG 2003 C 1 
HETATM 4 C C4 NAG . . . H 3 35.423 8.697 -90.929 1 277.23 ? C4 NAG 2003 C 1 
HETATM 5 C C5 NAG . . . H 3 34.331 9.734 -90.636 1 277.87 ? C5 NAG 2003 C 1 
HETATM 6 C C6 NAG . . . H 3 34.733 11.065 -91.287 1 284.27 ? C6 NAG 2003 C 1 
HETATM 7 C C7 NAG . . . H 3 33.758 5.993 -88.781 1 262.51 ? C7 NAG 2003 C 1 
HETATM 8 C C8 NAG . . . H 3 33.526 7.117 -87.801 1 261.88 ? C8 NAG 2003 C 1 
HETATM 9 N N2 NAG . . . H 3 33.075 6.023 -89.936 1 264.86 ? N2 NAG 2003 C 1 
HETATM 10 O O3 NAG . . . H 3 35.652 6.512 -91.923 1 274.84 ? O3 NAG 2003 C 1 
HETATM 11 O O4 NAG . . . H 3 36.502 8.878 -90.015 1 277.42 ? O4 NAG 2003 C 1 
HETATM 12 O O5 NAG . . . H 3 33.056 9.388 -91.16 1 276.12 ? O5 NAG 2003 C 1 
HETATM 13 O O6 NAG . . . H 3 34.866 10.911 -92.693 1 287.89 ? O6 NAG 2003 C 1 
HETATM 14 O O7 NAG . . . H 3 34.563 5.094 -88.51 1 260.52 ? O7 NAG 2003 C 1 
#
_model_server_stats.io_time_ms              81 
_model_server_stats.parse_time_ms           33 
_model_server_stats.create_model_time_ms    47 
_model_server_stats.query_time_ms           322 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           14 
#