MolNFT v1 · #152882 · protein
Crystal structure of rhesus macaque MHC class I molecule mamu-B*05104 complexed with C14-gggi lipopeptide
6IWH · MHC class I antigen: “Crystal structure of rhesus macaque MHC class I molecule mamu-B*05104 complexed with C14-gggi lipopeptide”. X-ray diffraction, 2 ligands (MYR, NA), 5 pockets (best druggability 0.72). MolNFT v1 #152882 on…
- PDB
- 6IWH
- 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; C14-gggi lipopeptide
- UniProt
- B2ZHY7, Q6V7J5
- Ligands
- MYR, NA
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% 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 | C14-gggi lipopeptide | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- MYR · Myristic acid · ligand · chains A, C
- NA · Sodium ion · metal · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 378 | 0.72 | 0.83 | 43 | MYR, EDO |
| 2 | 710 | 0.68 | 0.76 | 63 | NA, EDO |
| 3 | 115 | 0.44 | 0.78 | 25 | NA, EDO |
| 4 | 102 | 0.41 | 0.77 | 17 | empty |
| 5 | 54 | 0.29 | 0.75 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1302 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 344 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 lipid (disulfide, myristoylation).
Compared structures
- 6IWH · 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 6IWH · PDBe 6IWH · UniProt B2ZHY7 · UniProt Q6V7J5
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