Research workbench
HIV-1 nef in complex with MHC-I cytoplasmic domain and MU1 adaptin subunit of AP1 adaptor (second domain)
Analyse HIV-1 nef in complex with MHC-I cytoplasmic domain and MU1 adaptin subunit of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EMZ
- Type
- protein
- Length
- 826 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein nef; MHC-I; Ap-1 complex subunit mu-1
- UniProt
- Q90VU7, P35585
- Pockets
- 12 · best druggability 0.64
Structure
x-ray diffraction · 5 distinct chains · 20% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Protein nef | protein | 142 | 37% helix, 16% strand | Q90VU7 |
| D | MHC-I | protein | 19 | 0% helix, 21% strand | — |
| E | MHC-I | protein | 17 | 0% helix, 18% strand | — |
| B | Protein nef | protein | 138 | 38% helix, 14% strand | Q90VU7 |
| A, M | Ap-1 complex subunit mu-1 | protein | 255 | 4% helix, 60% strand | P35585 |
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.64 | 0.84 | 24 | empty |
| 2 | 333 | 0.63 | 0.79 | 35 | empty |
| 3 | 347 | 0.59 | 0.77 | 49 | empty |
| 4 | 210 | 0.57 | 0.80 | 24 | empty |
| 5 | 129 | 0.49 | 0.79 | 25 | empty |
Interfaces
9 interfaces between chains.
- B–A · 1232 Ų buried · 18 hydrogen bonds · protein-protein
- C–M · 1228 Ų buried · 14 hydrogen bonds · protein-protein
- D–M · 793 Ų buried · 17 hydrogen bonds · protein-protein
- E–A · 774 Ų buried · 18 hydrogen bonds · protein-protein
- C–A · 691 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 4EMZ · HIV-1 Nef in complex with MHC-I cytoplasmic domain and Mu1 adaptin subunit of AP1 adaptor… · the same entry in another collection · chain M against M, TM-score 1.00
- P35585 · AlphaFold monomer V2.0 prediction for ap-1 complex subunit mu-1 (P35585) · a predicted model of the same protein · chain M against A, TM-score 0.97
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 Q90VU7
- Every structure of UniProt P35585
- Elsewhere: RCSB PDB 4EMZ · PDBe 4EMZ · UniProt Q90VU7 · UniProt P35585
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