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Crystal structure of RNA dependent RNA polymerase domain from west nile virus

Analyse Crystal structure of RNA dependent RNA polymerase domain from west nile virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2HFZ
Type: protein
Length: 608 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA-directed RNA POLYMERASE(NS5)
EC: 2.7.7.48
UniProt: P14335
Ligands: MG, ZN
Pockets: 7 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA-directed RNA POLYMERASE(NS5) (EC 2.7.7.48)	protein	608	46% helix, 9% strand	P14335

Ligands and binding sites

MG · Magnesium ion · metal · chains A
ZN · Zinc ion · metal · chains A

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

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	621	0.74	0.81	68	empty
2	85	0.62	0.89	21	empty
3	147	0.56	0.82	26	empty
4	92	0.51	0.83	26	empty
5	67	0.44	0.82	17	empty

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

2HFZ · Crystal structure of RNA dependent RNA polymerase domain from West Nile virus · 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 P14335
Elsewhere: RCSB PDB 2HFZ · PDBe 2HFZ · UniProt P14335

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