MolNFT v1 · #101010 · protein

Crystal structure of ap-2 ALPHA/SIMGA2 complex bound to HIV-1 nef

4NEE · Ap-2 complex subunit sigma: “Crystal structure of ap-2 ALPHA/SIMGA2 complex bound to HIV-1 nef”. X-ray diffraction, 20 pockets (best druggability 0.82). MolNFT v1 #101010 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4NEE
Type: protein
Length: 2,681 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ap-2 complex subunit sigma; Ap-2 complex subunit alpha-2; Protein nef
UniProt: P62744, Q66HM2, Q90VU7
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 6 distinct chains · 61% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, L, F, I	Ap-2 complex subunit sigma	protein	142	46% helix, 27% strand	P62744
G, B, J	Ap-2 complex subunit alpha-2	protein	388	75% helix, 1% strand	Q66HM2
A	Ap-2 complex subunit alpha-2	protein	385	72% helix, 1% strand	Q66HM2
E, C	Protein nef	protein	139	41% helix, 12% strand	Q90VU7
H	Protein nef	protein	142	42% helix, 12% strand	Q90VU7
K	Protein nef	protein	144	42% helix, 11% strand	Q90VU7

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	849	0.82	0.84	91	empty
2	934	0.80	0.82	96	empty
3	684	0.79	0.84	69	empty
4	591	0.78	0.84	62	empty
5	113	0.74	0.94	24	empty

Interfaces

25 interfaces between chains.

L–J · 2526 Å² buried · 28 hydrogen bonds · protein-protein
D–B · 2518 Å² buried · 26 hydrogen bonds · protein-protein
F–A · 2505 Å² buried · 31 hydrogen bonds · protein-protein
I–G · 2491 Å² buried · 27 hydrogen bonds · protein-protein
F–E · 830 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

4NEE · crystal structure of AP-2 alpha/simga2 complex bound to HIV-1 Nef · the same entry in another collection · chain C against C, 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 P62744
Every structure of UniProt Q66HM2
Every structure of UniProt Q90VU7
Elsewhere: RCSB PDB 4NEE · PDBe 4NEE · UniProt P62744 · UniProt Q66HM2 · UniProt Q90VU7

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