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

Analyse Crystal structure of SIVMAC239 nef in an exxxlm endocytic sorting motif bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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

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Every structure of UniProt Q5QGG3
Elsewhere: RCSB PDB 5NUI · PDBe 5NUI · UniProt Q5QGG3

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