MolNFT v1 · #88617 · protein
Complex of a B21 chicken MHC class I molecule and a 10MER chicken peptide
4D0C · MHC class I alpha chain 2: “Complex of a B21 chicken MHC class I molecule and a 10MER chicken peptide”. X-ray diffraction, 3 pockets (best druggability 0.69). MolNFT v1 #88617 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4D0C
- Type
- protein
- Length
- 383 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I alpha chain 2; Beta-2-microglobulin; 10MER peptide
- UniProt
- Q95601, P21611
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I alpha chain 2 | protein | 276 | 27% helix, 38% strand | Q95601 |
| B | Beta-2-microglobulin | protein | 97 | 0% helix, 49% strand | P21611 |
| C | 10MER peptide | protein | 10 | 40% helix, 0% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 504 | 0.69 | 0.80 | 61 | empty |
| 2 | 63 | 0.29 | 0.74 | 15 | empty |
| 3 | 51 | 0.25 | 0.73 | 13 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1700 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 891 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4D0C · Complex of a B21 chicken MHC class I molecule and a 10MER chicken peptide · the same entry in another collection · chain A against A, TM-score 1.00
- P21611 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P21611) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q95601
- Every structure of UniProt P21611
- Elsewhere: RCSB PDB 4D0C · PDBe 4D0C · UniProt Q95601 · UniProt P21611
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