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Crystal structure of rice dwarf virus P5 in space group P212121

Analyse Crystal structure of rice dwarf virus P5 in space group P212121 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5X71
Type: protein
Length: 1,591 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MRNA capping enzyme P5
EC: 2.7.7.50
Ligands: 5GP
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MRNA capping enzyme P5 (EC 2.7.7.50)	protein	796	40% helix, 18% strand	—
B	MRNA capping enzyme P5 (EC 2.7.7.50)	protein	795	40% helix, 18% strand	—

Ligands and binding sites

5GP · Guanosine-5'-monophosphate · ligand · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	524	0.81	0.87	67	empty
2	512	0.80	0.86	66	empty
3	568	0.79	0.85	78	empty
4	796	0.77	0.81	42	empty
5	91	0.77	0.98	19	empty

Interfaces

1 interface between chains.

A–B · 3153 Å² buried · 47 hydrogen bonds · protein-protein

Compared structures

5X71 · Crystal structure of Rice Dwarf Virus P5 in space group P212121 · 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
Elsewhere: RCSB PDB 5X71 · PDBe 5X71

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