Research workbench

HIV-1 nef protein in complex with R96I mutant fyn SH3 domain

Analyse HIV-1 nef protein in complex with R96I mutant fyn SH3 domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1EFN
Type: protein
Length: 322 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fyn tyrosine kinase; HIV-1 nef protein
EC: 2.7.1.112
UniProt: P06241, P03406
Ligands: PBM
Pockets: 3 · best druggability 0.55

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Fyn tyrosine kinase (EC 2.7.1.112)	protein	57	5% helix, 49% strand	P06241
B, D	HIV-1 nef protein	protein	104	38% helix, 14% strand	P03406

Ligands and binding sites

PBM · Trimethyl lead ion · ligand · 2 copies · chains B, D

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

Pockets

3 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	221	0.55	0.78	30	PBM
2	89	0.35	0.75	17	empty
3	82	0.33	0.74	14	empty

Interfaces

3 interfaces between chains.

A–B · 651 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 626 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 398 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

1EFN · HIV-1 nef protein in complex with R96I mutant fyn SH3 domain · the same entry in another collection · chain A against A, TM-score 1.00
P06241 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase fyn (P06241) · a predicted model of the same protein · chain C against A, TM-score 0.95

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 P06241
Every structure of UniProt P03406
Elsewhere: RCSB PDB 1EFN · PDBe 1EFN · UniProt P06241 · UniProt P03406

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