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MolNFT v1 · #128561 · protein

Crystal structure of SIVMAC239 nef in an exxxlm endocytic sorting motif bound state

5NUI · Protein nef: “Crystal structure of SIVMAC239 nef in an exxxlm endocytic sorting motif bound state”. X-ray diffraction, 4 pockets (best druggability 0.61). MolNFT v1 #128561 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5NUI
Type: protein
Length: 246 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein nef; Ser-gln-ile-lys-arg-leu-leu-ser
UniProt: Q5QGG3
Pockets: 4 · best druggability 0.61

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein nef	protein	108	37% helix, 15% strand	Q5QGG3
B	Protein nef	protein	130	42% helix, 12% strand	Q5QGG3
M	Ser-gln-ile-lys-arg-leu-leu-ser	protein	8	50% helix, 0% strand	—

Pockets

4 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	339	0.61	0.78	41	empty
2	55	0.48	0.85	14	empty
3	76	0.40	0.78	18	empty
4	81	0.39	0.77	17	empty

Interfaces

3 interfaces between chains.

A–B · 550 Å² buried · 5 hydrogen bonds · protein-protein
B–M · 235 Å² buried · 1 hydrogen bond · protein-protein
A–M · 73 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5NUI · Crystal structure of SIVmac239 Nef in an ExxxLM endocytic sorting motif bound state · 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 Q5QGG3
Elsewhere: RCSB PDB 5NUI · PDBe 5NUI · UniProt Q5QGG3

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