MolNFT v1 · #115645 · protein

Crystal structure of murine polyomavirus pta strain VP1

5CPU: “Crystal structure of murine polyomavirus pta strain VP1”. X-ray diffraction, 20 pockets (best druggability 0.66). MolNFT v1 #115645 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5CPU
Type: protein
Length: 1,396 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VP1
UniProt: Q76TX8
Pockets: 20 · best druggability 0.66

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	VP1	protein	279	8% helix, 39% strand	Q76TX8
B, C, E	VP1	protein	278	8% helix, 39% strand	Q76TX8
D	VP1	protein	283	8% helix, 39% strand	Q76TX8

Ligands and binding sites

GOL · Glycerol · additive · 7 copies · chains A, B, C, D, E

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	121	0.66	0.89	30	empty
2	125	0.66	0.89	28	empty
3	115	0.66	0.89	29	empty
4	124	0.65	0.88	31	empty
5	105	0.63	0.88	22	empty

Interfaces

5 interfaces between chains.

A–B · 2264 Å² buried · 34 hydrogen bonds · protein-protein
A–E · 2247 Å² buried · 30 hydrogen bonds · protein-protein
B–C · 2237 Å² buried · 32 hydrogen bonds · protein-protein
D–E · 2231 Å² buried · 33 hydrogen bonds · protein-protein
C–D · 2216 Å² buried · 32 hydrogen bonds · protein-protein

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 Q76TX8
Elsewhere: RCSB PDB 5CPU · PDBe 5CPU · UniProt Q76TX8

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