MolNFT v1 · #107287 · protein

Crystal structure of HIV-1 nef-SF2 core domain in complex with the src family kinase hck SH3-SH2 tandem regulatory domains

4U5W · Protein nef: “Crystal structure of HIV-1 nef-SF2 core domain in complex with the src family kinase hck SH3-SH2 tandem…”. X-ray diffraction, 1 ligand (IOD), 7 pockets (best druggability 0.78). MolNFT v1 #107287 on GenesisL1: 3D…

PDB: 4U5W
Type: protein
Length: 550 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein nef; Tyrosine-protein kinase hck
EC: 2.7.10.2
UniProt: P03407, P08631
Ligands: IOD
Pockets: 7 · best druggability 0.78

Structure

x-ray diffraction · 4 distinct chains · 23% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein nef	protein	116	33% helix, 12% strand	P03407
B	Tyrosine-protein kinase hck (EC 2.7.10.2)	protein	163	15% helix, 37% strand	P08631
C	Protein nef	protein	111	36% helix, 13% strand	P03407
D	Tyrosine-protein kinase hck (EC 2.7.10.2)	protein	160	16% helix, 35% strand	P08631

Ligands and binding sites

IOD · Iodide ion · ion · 6 copies · chains A, D, B, C
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, B, D, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	109	0.78	0.97	21	MPD
2	903	0.78	0.81	80	MPD
3	232	0.58	0.79	28	empty
4	181	0.55	0.80	28	empty
5	137	0.46	0.76	19	empty

Interfaces

6 interfaces between chains.

A–C · 958 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 932 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 896 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 277 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 231 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4U5W · Crystal Structure of HIV-1 Nef-SF2 Core Domain in Complex with the Src Family Kinase Hck… · the same entry in another collection · chain A against A, TM-score 1.00
P08631 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase hck (P08631) · a predicted model of the same protein · chain B against A, TM-score 0.72

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 P03407
Every structure of UniProt P08631
Elsewhere: RCSB PDB 4U5W · PDBe 4U5W · UniProt P03407 · UniProt P08631

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