MolNFT v1 · #77642 · protein
HIV nef derived peptide NEF73 complexed to HLA-A*0301
3RL2 · HLA class I histocompatibility antigen, a-3 alpha chain: “HIV nef derived peptide NEF73 complexed to HLA-A*0301”. X-ray diffraction, 4 pockets (best druggability 0.66). MolNFT v1 #77642 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3RL2
- Type
- protein
- Length
- 383 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-3 alpha chain; Beta-2-microglobulin; NEF73…
- UniProt
- P04439, P61769, Q9YYU8
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-3 alpha chain | protein | 274 | 23% helix, 39% strand | P04439 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 52% strand | P61769 |
| C | NEF73 peptide from protein nef | protein | 10 | 0% helix, 0% strand | Q9YYU8 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 482 | 0.66 | 0.78 | 50 | empty |
| 2 | 82 | 0.45 | 0.81 | 17 | empty |
| 3 | 90 | 0.45 | 0.80 | 23 | empty |
| 4 | 73 | 0.34 | 0.76 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1406 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1003 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3RL2 · HIV Nef derived peptide Nef73 complexed to HLA-A*0301 · the same entry in another collection · chain A against A, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P04439 · AlphaFold monomer V2.0 prediction for HLA class I histocompatibility antigen, a alpha… · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P04439
- Every structure of UniProt P61769
- Every structure of UniProt Q9YYU8
- Elsewhere: RCSB PDB 3RL2 · PDBe 3RL2 · UniProt P04439 · UniProt P61769 · UniProt Q9YYU8
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