MolNFT v1 · #113426 · protein

Crystal structure of the C-terminal 2',5'-phosphodiesterase domain of group a rotavirus protein VP3

5AF2: “Crystal structure of the C-terminal 2',5'-phosphodiesterase domain of group a rotavirus protein VP3”. X-ray diffraction, 1 ligand (K), 4 pockets (best druggability 0.46). MolNFT v1 #113426 on GenesisL1: 3D structure, binding sites…

PDB: 5AF2
Type: protein
Length: 564 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VP3
UniProt: A2T3S1
Ligands: K
Pockets: 4 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain · 22% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	VP3	protein	141	22% helix, 40% strand	A2T3S1

Ligands and binding sites

K · Potassium ion · metal · 2 copies
15P · Polyethylene glycol (N=34) · additive · chains A

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

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	163	0.46	0.76	21	empty
2	163	0.43	0.74	24	empty
3	149	0.40	0.73	23	empty
4	76	0.33	0.74	21	empty

Interfaces

5 interfaces between chains.

A–C · 330 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 64 Å² buried · 1 hydrogen bond · protein-protein
A–B · 58 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 54 Å² buried · 1 hydrogen bond · protein-protein
B–C · 31 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5AF2 · Crystal structure of the C-terminal 2',5'-phosphodiesterase domain of group A rotavirus… · 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 A2T3S1
Elsewhere: RCSB PDB 5AF2 · PDBe 5AF2 · UniProt A2T3S1

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