MolNFT v1 · #54461 · protein + RNA

Crystal structure of physalis mottle virus with intact ordered RNA

2XPJ · Coat protein: “Crystal structure of physalis mottle virus with intact ordered RNA”. X-ray diffraction, 3 pockets (best druggability 0.53). MolNFT v1 #54461 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2XPJ
Type: protein + RNA
Length: 533 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coat protein; 5'-R(CP*CP*CP)-3'
UniProt: P36351
Pockets: 3 · best druggability 0.53

Structure

x-ray diffraction · 4 distinct chains · 10% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Coat protein	protein	165	10% helix, 42% strand	P36351
B	Coat protein	protein	180	10% helix, 45% strand	P36351
C	Coat protein	protein	185	10% helix, 42% strand	P36351
D	5'-R(CPCPCP)-3'	rna	3	—	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	218	0.53	0.77	32	empty
2	85	0.42	0.79	25	empty
3	56	0.28	0.75	15	empty

Interfaces

4 interfaces between chains.

B–C · 995 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 739 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 699 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 244 Å² buried · 4 hydrogen bonds · protein-nucleic

Compared structures

2XPJ · Crystal structure of Physalis Mottle Virus with intact ordered RNA · 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 P36351
Elsewhere: RCSB PDB 2XPJ · PDBe 2XPJ · UniProt P36351

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