Research workbench
Crystal structure of psla-1*0401 complex with dodecapeptide rvedvtntaeyw
Analyse Crystal structure of psla-1*0401 complex with dodecapeptide rvedvtntaeyw in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LF8
- Type
- protein
- Length
- 384 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Arg-val-glu-asp-val-thr-asn-thr-ala-glu-tyr-TRP
- UniProt
- A0A0F6N4U7, Q07717
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 275 | 27% helix, 37% strand | A0A0F6N4U7 |
| B | Beta-2-microglobulin | protein | 97 | 0% helix, 53% strand | Q07717 |
| C | Arg-val-glu-asp-val-thr-asn-thr-ala-glu-tyr-TRP | protein | 12 | 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 | 550 | 0.69 | 0.79 | 48 | empty |
| 2 | 164 | 0.48 | 0.77 | 25 | empty |
| 3 | 56 | 0.42 | 0.83 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1376 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1140 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6LF8 · Crystal structure of pSLA-1*0401 complex with dodecapeptide RVEDVTNTAEYW · 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 A0A0F6N4U7
- Every structure of UniProt Q07717
- Elsewhere: RCSB PDB 6LF8 · PDBe 6LF8 · UniProt A0A0F6N4U7 · UniProt Q07717
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