MolNFT v1 · #118431 · protein
MHC complexed to 11MER peptide
5F1N · MHC class I antigen: “MHC complexed to 11MER peptide”. X-ray diffraction, 11 pockets (best druggability 0.74). MolNFT v1 #118431 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5F1N
- Type
- protein
- Length
- 770 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Peptide from cytochrome P450 family 1…
- UniProt
- J9UGS3, E2RN10, C1KG39
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | MHC class I antigen | protein | 275 | 27% helix, 40% strand | J9UGS3 |
| B, E | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | E2RN10 |
| C, F | Peptide from cytochrome P450 family 1 subfamily B polypeptide 1 | protein | 11 | 27% helix, 0% strand | C1KG39 |
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.74 | 0.98 | 20 | empty |
| 2 | 737 | 0.73 | 0.79 | 75 | empty |
| 3 | 598 | 0.69 | 0.78 | 55 | empty |
| 4 | 256 | 0.54 | 0.77 | 24 | empty |
| 5 | 161 | 0.49 | 0.78 | 28 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1320 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1293 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1122 Ų buried · 18 hydrogen bonds · protein-protein
- D–F · 1095 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 871 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5F1N · MHC complexed to 11mer peptide · the same entry in another collection · chain A against A, TM-score 1.00
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 J9UGS3
- Every structure of UniProt E2RN10
- Every structure of UniProt C1KG39
- Elsewhere: RCSB PDB 5F1N · PDBe 5F1N · UniProt J9UGS3 · UniProt E2RN10 · UniProt C1KG39
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