Research workbench
MHC with 9-mer peptide
Analyse MHC with 9-mer peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F1I
- Type
- protein
- Length
- 3,030 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I dla-88; BETA2M; 9-mer peptide
- UniProt
- J9UGS3
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, J | MHC class I dla-88 | protein | 270 | 26% helix, 39% strand | J9UGS3 |
| B, E, H, K, N, Q, T, W | BETA2M | protein | 99 | 0% helix, 53% strand | — |
| C, F, I, L, O, R, U, X | 9-mer peptide | protein | 9 | 0% helix, 0% strand | — |
| D, G, M, P, S, V | MHC class I dla-88 | protein | 271 | 27% helix, 39% strand | J9UGS3 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.82 | 0.97 | 27 | empty |
| 2 | 865 | 0.78 | 0.81 | 88 | empty |
| 3 | 1149 | 0.77 | 0.79 | 93 | empty |
| 4 | 1199 | 0.77 | 0.79 | 107 | empty |
| 5 | 890 | 0.77 | 0.80 | 87 | empty |
Interfaces
46 interfaces between chains.
- V–W · 1326 Ų buried · 21 hydrogen bonds · protein-protein
- M–N · 1312 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1297 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 1290 Ų buried · 17 hydrogen bonds · protein-protein
- P–Q · 1270 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 5F1I · MHC with 9-mer 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
- Elsewhere: RCSB PDB 5F1I · PDBe 5F1I · UniProt J9UGS3
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