MolNFT v1 · #135187 · protein

Crystal structure of the hepatitis C virus NS5B RNA-dependent RNA polymerase in complex with 2-{[2-(CARBOXYMETHOXY)BENZENE-1- CARBONYL]AMINO}-3-[(4-CHLOROPHENYL)METHOXY]BENZOIC acid

5TRJ: “Crystal structure of the hepatitis C virus NS5B RNA-dependent RNA polymerase in complex with…”. X-ray diffraction, 3 ligands (23E, 7HO, SO4), 17 pockets (best druggability 0.78). MolNFT v1 #135187 on GenesisL1: 3D structure, binding…

PDB: 5TRJ
Type: protein
Length: 1,094 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA-dependent RNA polymerase
EC: 2.7.7.48
UniProt: Q9WMX2
Ligands: 23E, 7HO, SO4
Pockets: 17 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA-dependent RNA polymerase (EC 2.7.7.48)	protein	551	47% helix, 15% strand	Q9WMX2
B	RNA-dependent RNA polymerase (EC 2.7.7.48)	protein	543	47% helix, 15% strand	Q9WMX2

Ligands and binding sites

23E · (2E)-3-(4-{[(1-{[(13-cyclohexyl-6-oxo-6,7-dihydro-5H-indolo[1,2-d][1,4]benzodiazepin-10-yl)carbonyl]amino}cyclopentyl)carbonyl]amino}phenyl)prop-2-enoic acid · ligand · 2 copies · chains A, B
7HO · 2-{[2-(carboxymethoxy)benzene-1-carbonyl]amino}-3-[(4-chlorophenyl)methoxy]benzoic acid · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 10 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

17 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	847	0.78	0.81	74	7HO, SO4
2	1185	0.76	0.79	83	7HO, SO4
3	110	0.45	0.79	21	empty
4	84	0.44	0.80	23	empty
5	110	0.43	0.77	17	empty

Interfaces

1 interface between chains.

A–B · 974 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

5TRJ · CRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS NS5B RNA-DEPENDENT RNA POLYMERASE IN COMPLEX… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9WMX2
Elsewhere: RCSB PDB 5TRJ · PDBe 5TRJ · UniProt Q9WMX2

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