PDBsum entry 5fpt

Hydrolase

PDB id: 5fpt

Contents

Protein chains

645 a.a.

Ligands

3VY ×2

Waters ×463

PDB id:

5fpt

Name:

Hydrolase

Title:

Structure of hepatitis c virus (hcv) full-length ns3 complex with small-molecule ligand 2-(1-methyl-1h-indol-3-yl)acetic acid (at3437) in an alternate binding site.

Structure:

Hepatitis c virus full-length ns3 complex. Chain: a, b. Engineered: yes

Source:

Hepatitis c virus (isolate bk). Organism_taxid: 11105. Strain: genotype 1b. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

2.72Å R-factor: 0.160 R-free: 0.251

Authors:

H.Jhoti,R.F.Ludlow,H.K.Saini,I.J.Tickle,M.Verdonk,P.Pathuri, P.A.Williams

Key ref:

R.F.Ludlow et al. (2015). Detection of secondary binding sites in proteins using fragment screening. Proc Natl Acad Sci U S A, 112, 15910-15915. PubMed id: 26655740 DOI: 10.1073/pnas.1518946112

Date:

02-Dec-15 Release date: 23-Dec-15

Protein chains

P26663  (POLG_HCVBK) -  Genome polyprotein from Hepatitis C virus genotype 1b (isolate BK)

Seq: 3010 a.a.

Struc: 645 a.a.*

* PDB and UniProt seqs differ at 18 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 2: E.C.3.4.21.98 - hepacivirin.
• Reaction: Hydrolysis of four peptide bonds in the viral precursor polyprotein, commonly with Asp or Glu in the P6 position, Cys or Thr in P1 and Ser or Ala in P1'.
• Enzyme class 3: E.C.3.4.22.- - ?????
• Enzyme class 4: E.C.3.6.1.15 - nucleoside-triphosphate phosphatase.
• Reaction: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H⁺
• Enzyme class 5: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1073/pnas.1518946112

Proc Natl Acad Sci U S A 112:15910-15915 (2015)

PubMed id: 26655740

Detection of secondary binding sites in proteins using fragment screening.

R.F.Ludlow, M.L.Verdonk, H.K.Saini, I.J.Tickle, H.Jhoti.

ABSTRACT

Proteins need to be tightly regulated as they control biological processes in most normal cellular functions. The precise mechanisms of regulation are rarely completely understood but can involve binding of endogenous ligands and/or partner proteins at specific locations on a protein that can modulate function. Often, these additional secondary binding sites appear separate to the primary binding site, which, for example for an enzyme, may bind a substrate. In previous work, we have uncovered several examples in which secondary binding sites were discovered on proteins using fragment screening approaches. In each case, we were able to establish that the newly identified secondary binding site was biologically relevant as it was able to modulate function by the binding of a small molecule. In this study, we investigate how often secondary binding sites are located on proteins by analyzing 24 protein targets for which we have performed a fragment screen using X-ray crystallography. Our analysis shows that, surprisingly, the majority of proteins contain secondary binding sites based on their ability to bind fragments. Furthermore, sequence analysis of these previously unknown sites indicate high conservation, which suggests that they may have a biological function, perhaps via an allosteric mechanism. Comparing the physicochemical properties of the secondary sites with known primary ligand binding sites also shows broad similarities indicating that many of the secondary sites may be druggable in nature with small molecules that could provide new opportunities to modulate potential therapeutic targets.