Research workbench
Crystal structure of ap-2 ALPHA/SIMGA2 complex bound to HIV-1 nef
Analyse Crystal structure of ap-2 ALPHA/SIMGA2 complex bound to HIV-1 nef in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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.
| Volume (ų) | 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 Ų buried · 28 hydrogen bonds · protein-protein
- D–B · 2518 Ų buried · 26 hydrogen bonds · protein-protein
- F–A · 2505 Ų buried · 31 hydrogen bonds · protein-protein
- I–G · 2491 Ų buried · 27 hydrogen bonds · protein-protein
- F–E · 830 Ų 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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