Research workbench
Crystal structure of rhesus macaque MHC class I molecule mamu-B*098 complexed with mono-acyl glycerol
Analyse Crystal structure of rhesus macaque MHC class I molecule mamu-B*098 complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LB2
- Type
- protein
- Length
- 754 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin
- UniProt
- A0A1E1GJG5, Q6V7J5
- Ligands
- EKG, ZN
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | MHC class I antigen | protein | 277 | 28% helix, 39% strand | A0A1E1GJG5 |
| B, D | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | Q6V7J5 |
Ligands and binding sites
- EKG · (2R)-2,3-dihydroxypropyl hexadecanoate · ligand · 2 copies · chains A, C
- ZN · Zinc ion · metal · 7 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 41 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1087 | 0.74 | 0.77 | 91 | EDO |
| 2 | 612 | 0.69 | 0.77 | 60 | EDO |
| 3 | 378 | 0.67 | 0.80 | 35 | EDO, EKG |
| 4 | 346 | 0.66 | 0.80 | 38 | EDO, EKG |
| 5 | 291 | 0.55 | 0.76 | 42 | EDO |
Interfaces
4 interfaces between chains.
- A–B · 1347 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1301 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 240 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 44 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6LB2 · Crystal structure of rhesus macaque MHC class I molecule Mamu-B*098 complexed with… · the same entry in another collection · chain B against B, 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 0.99
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 A0A1E1GJG5
- Every structure of UniProt Q6V7J5
- Elsewhere: RCSB PDB 6LB2 · PDBe 6LB2 · UniProt A0A1E1GJG5 · UniProt Q6V7J5
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