MolNFT v1 · #25373 · protein

Unassembled polyomavirus VP1 pentamer

1VPN: “Unassembled polyomavirus VP1 pentamer”. X-ray diffraction, 20 pockets (best druggability 0.67). MolNFT v1 #25373 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1VPN
Type: protein
Length: 1,429 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polyomavirus VP1 pentamer
UniProt: P49302
Pockets: 20 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D, E	Polyomavirus VP1 pentamer	protein	285	7% helix, 39% strand	P49302
B	Polyomavirus VP1 pentamer	protein	289	7% helix, 40% strand	P49302

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	110	0.67	0.91	27	empty
2	101	0.67	0.91	29	empty
3	116	0.66	0.90	29	empty
4	130	0.66	0.88	29	empty
5	107	0.64	0.89	29	empty

Interfaces

5 interfaces between chains.

B–C · 2362 Å² buried · 31 hydrogen bonds · protein-protein
D–E · 2340 Å² buried · 30 hydrogen bonds · protein-protein
A–B · 2338 Å² buried · 32 hydrogen bonds · protein-protein
C–D · 2329 Å² buried · 29 hydrogen bonds · protein-protein
A–E · 2326 Å² buried · 32 hydrogen bonds · protein-protein

Compared structures

1VPN · Unassembled polyomavirus VP1 pentamer · 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 P49302
Elsewhere: RCSB PDB 1VPN · PDBe 1VPN · UniProt P49302

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