MolNFT v1 · #152881 · protein
Crystal structure of rhesus macaque MHC class I molecule mamu-B*05104 complexed with N-myristoylated 4-mer lipopeptide derived from SIV nef protein
6IWG · MHC class I antigen: “Crystal structure of rhesus macaque MHC class I molecule mamu-B*05104 complexed with N-myristoylated 4-mer…”. X-ray diffraction, 3 ligands (MYR, NA, BO3), 6 pockets (best druggability 0.71). MolNFT v1 #152881…
- PDB
- 6IWG
- Type
- protein
- Length
- 380 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; N-myristoylated 4-mer lipopeptide
- UniProt
- B2ZHY7, Q6V7J5
- Ligands
- MYR, NA, BO3
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 276 | 26% helix, 39% strand | B2ZHY7 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | Q6V7J5 |
| C | N-myristoylated 4-mer lipopeptide | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- MYR · Myristic acid · ligand · chains A, C
- NA · Sodium ion · metal · 4 copies · chains A, B
- BO3 · Boric acid · ion · 3 copies · chains B
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 350 | 0.71 | 0.83 | 38 | MYR, EDO |
| 2 | 727 | 0.70 | 0.77 | 58 | NA, EDO, BO3 |
| 3 | 102 | 0.44 | 0.79 | 19 | EDO |
| 4 | 90 | 0.42 | 0.78 | 16 | empty |
| 5 | 54 | 0.31 | 0.76 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1289 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 361 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 lipid (disulfide, myristoylation).
Compared structures
- 6IWG · Crystal structure of rhesus macaque MHC class I molecule Mamu-B*05104 complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6V7J5 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (Q6V7J5) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 B2ZHY7
- Every structure of UniProt Q6V7J5
- Elsewhere: RCSB PDB 6IWG · PDBe 6IWG · UniProt B2ZHY7 · UniProt Q6V7J5
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