Research workbench
Uncommon structural features of rabbit MHC class I (rla-A1) complexed with rabbit haemorrhagic disease virus (rhdv) derived peptide, VP60- 10
Analyse Uncommon structural features of rabbit MHC class I (rla-A1) complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M2K
- Type
- protein
- Length
- 383 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP60-10; Beta-2-microglobulin; Rla class I histocompatibility antigen, alpha chain 19-1
- UniProt
- P61769, P06140
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | VP60-10 | protein | 9 | 0% helix, 0% strand | — |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| A | Rla class I histocompatibility antigen, alpha chain 19-1 | protein | 274 | 28% helix, 40% strand | P06140 |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 549 | 0.66 | 0.77 | 51 | empty |
| 2 | 79 | 0.48 | 0.83 | 19 | empty |
| 3 | 101 | 0.40 | 0.77 | 17 | empty |
| 4 | 51 | 0.39 | 0.81 | 16 | empty |
| 5 | 53 | 0.33 | 0.77 | 15 | empty |
Interfaces
2 interfaces between chains.
- B–A · 1367 Ų buried · 20 hydrogen bonds · protein-protein
- C–A · 839 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6M2K · Uncommon structural features of rabbit MHC class I (RLA-A1) complexed with rabbit… · the same entry in another collection · chain C against C, TM-score 1.00
- P06140 · AlphaFold monomer V2.0 prediction for rla class I histocompatibility antigen, alpha chain… · a predicted model of the same protein · chain A against A, TM-score 0.98
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P61769
- Every structure of UniProt P06140
- Elsewhere: RCSB PDB 6M2K · PDBe 6M2K · UniProt P61769 · UniProt P06140
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