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Crystal Structure of viral RdRp in complex with GTP

Analyse Crystal Structure of viral RdRp in complex with GTP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4HDG
Type: protein
Length: 1,224 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.38
Source: Japanese encephalitis virus
Molecule: Polyprotein
EC: 2.7.7.48
UniProt: G3LHD9
Ligands: GTP, ZN
Pockets: 10 · best druggability 0.87

Structure

x-ray diffraction · resolution 2.38 · 1 distinct chain · 47% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Polyprotein (EC 2.7.7.48)	protein	612	47% helix, 12% strand	G3LHD9

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 4 copies · chains A, B

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

Pockets

10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	858	0.87	0.90	108	empty
2	836	0.86	0.88	85	GTP
3	431	0.83	0.91	68	GTP
4	115	0.66	0.89	25	empty
5	51	0.62	0.93	16	empty

Interfaces

1 interface between chains.

A–B · 1308 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

4HDG · Crystal structure of viral rdrp in complex 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 G3LHD9
Elsewhere: RCSB PDB 4HDG · PDBe 4HDG · UniProt G3LHD9

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