Structure of PDB 2vbm Chain A Binding Site BS01

Receptor Information

>2vbm Chain A (length=509) Species: 10761 (Lederbergvirus Sf6)

GPDLIEQLAQSGKYSQDNTKGDAMIGVKQPLPKAVLRTQHDKNKEAISIL
DFGVIDDGVTDNYQAIQNAIDAVASLPSGGELFIPASNQAVGYIVGSTLL
IPGGVNIRGVGKASQLRAKSGLTGSVLRLSYDSDTIGRYLRNIRVTGNNT
CNGIDTNITAEDSVIRQVYGWVFDNVMVNEVETAYLMQGLWHSKFIACQA
GTCRVGLHFLGQCVSVSVSSCHFSRGNYSADESFGIRIQPQTYAWSSEAV
RSEAIILDSETMCIGFKNAVYVHDCLDLHMEQLDLDYCGSTGVVIENVNG
GFSFSNSWIAADADGTEQFTGIYFRTPTSTQSHKIVSGVHINTANKNTAA
NNQSIAIEQSAIFVFVSGCTLTGDEWAVNIVDINECVSFDKCIFNKPLRY
LRSGGVSVTDCYLAGITEVQKPEGRYNTYRGCSGVPSVNGIINVPVAVGA
TSGSAAIPNPGNLTYRVRSLFGDPASSGDKVSVSGVTINVTRPSPVGVAL
PSMVEYLAI

Ligand information

• Ligand ID: RAM
• InChI: InChI=1S/C6H12O5/c1-2-3(7)4(8)5(9)6(10)11-2/h2-10H,1H3/t2-,3-,4+,5+,6+/m0/s1
• InChIKey: SHZGCJCMOBCMKK-HGVZOGFYSA-N
• SMILES:
  CACTVS 3.341: C[C@@H]1O[C@@H](O)[C@H](O)[C@H](O)[C@H]1O
  ACDLabs 10.04: OC1C(O)C(OC(O)C1O)C
  OpenEye OEToolkits 1.5.0: C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O)O)O)O
  OpenEye OEToolkits 1.5.0: CC1C(C(C(C(O1)O)O)O)O
  CACTVS 3.341: C[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
• Formula: C6 H12 O5
• Name: alpha-L-rhamnopyranose;
  alpha-L-rhamnose;
  6-deoxy-alpha-L-mannopyranose;
  L-rhamnose;
  rhamnose
• ZINC: ZINC000003861280
• PDB chain: 2vbm Chain B Residue 4

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2vbm An Intersubunit Active Site between Supercoiled Parallel Beta Helices in the Trimeric Tailspike Endorhamnosidase of Shigella Flexneri Phage Sf6.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): A203 R230 E293
• Binding residue (residue number reindexed from 1): A90 R117 E180
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 3.2.1.-

External links

• PDB: RCSB:2vbm, PDBe:2vbm, PDBj:2vbm
• PDBsum: 2vbm
• PubMed: 18462681
• UniProt: Q9XJP3|FIBER_BPSFV Tail spike protein