MolNFT v1 · #54215 · protein

HCV-H77 NS5B polymerase complexed with GTP

2XI3 · RNA-directed RNA polymerase: “HCV-H77 NS5B polymerase complexed with GTP”. X-ray diffraction, 2 ligands (GTP, MG), 12 pockets (best druggability 0.80). MolNFT v1 #54215 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2XI3
Type: protein
Length: 1,124 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA-directed RNA polymerase
EC: 2.7.7.48
UniProt: P27958
Ligands: GTP, MG
Pockets: 12 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	RNA-directed RNA polymerase (EC 2.7.7.48)	protein	562	50% helix, 15% strand	P27958

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 5 copies · chains A, B
MG · Magnesium ion · metal · 5 copies · chains A, B

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

Pockets

12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1084	0.80	0.81	81	GTP
2	1086	0.80	0.81	81	GTP, MG
3	862	0.76	0.80	87	empty
4	72	0.45	0.82	14	empty
5	58	0.39	0.80	15	empty

Interfaces

1 interface between chains.

A–B · 440 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

2XI3 · HCV-H77 NS5B Polymerase Complexed With GTP · 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 P27958
Elsewhere: RCSB PDB 2XI3 · PDBe 2XI3 · UniProt P27958

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