MolNFT v1 · #155090 · protein
Crystal structure of psla-1*1301(F99Y) complex with S-oiv-derived epitope nsdtvgwsw
6KWN · MHC class I antigen: “Crystal structure of psla-1*1301(F99Y) complex with S-oiv-derived epitope nsdtvgwsw”. X-ray diffraction, 3 pockets (best druggability 0.69). MolNFT v1 #155090 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6KWN
- Type
- protein
- Length
- 381 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Peptide
- UniProt
- B1PJU7, Q07717
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 275 | 27% helix, 39% strand | B1PJU7 |
| B | Beta-2-microglobulin | protein | 97 | 0% helix, 51% strand | Q07717 |
| C | Peptide | protein | 9 | 0% helix, 0% strand | — |
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 | 580 | 0.69 | 0.79 | 53 | empty |
| 2 | 151 | 0.44 | 0.75 | 21 | empty |
| 3 | 84 | 0.43 | 0.80 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1392 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 905 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6KWN · Crystal structure of pSLA-1*1301(F99Y) complex with S-OIV-derived epitope NSDTVGWSW · the same entry in another collection · chain A against A, TM-score 1.00
- Q07717 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (Q07717) · 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 B1PJU7
- Every structure of UniProt Q07717
- Elsewhere: RCSB PDB 6KWN · PDBe 6KWN · UniProt B1PJU7 · UniProt Q07717
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