MolNFT v1 · #156094 · protein
Crystal structure of rhesus macaque MHC class I molecule mamu-B*05104 complexed with lysophosphatidylcholine
6LT6 · MHC class I antigen: “Crystal structure of rhesus macaque MHC class I molecule mamu-B*05104 complexed with lysophosphatidylcholine”. X-ray diffraction, 2 ligands (EKG, NA), 5 pockets (best druggability 0.70). MolNFT v1 #156094 on…
- PDB
- 6LT6
- Type
- protein
- Length
- 376 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin
- UniProt
- B2ZHY7, Q6V7J5
- Ligands
- EKG, NA
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 2 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 |
Ligands and binding sites
- EKG · (2R)-2,3-dihydroxypropyl hexadecanoate · ligand · chains A
- NA · Sodium ion · metal · chains B
- EDO · 1,2-ethanediol · additive · 8 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 | 391 | 0.70 | 0.82 | 44 | EKG |
| 2 | 642 | 0.69 | 0.78 | 53 | EDO |
| 3 | 87 | 0.42 | 0.79 | 19 | empty |
| 4 | 67 | 0.40 | 0.79 | 16 | empty |
| 5 | 50 | 0.38 | 0.81 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1408 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6LT6 · 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 6LT6 · PDBe 6LT6 · UniProt B2ZHY7 · UniProt Q6V7J5
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