MolNFT v2 · #157413 · protein
Uncommon structural features of rabbit MHC class I (RLA-A1) complexed with rabbit haemorrhagic disease virus (RHDV) derived peptide, VP60-2
6M24 · RLA class I histocompatibility antigen, alpha chain 19-1: “Uncommon structural features of rabbit MHC class I (RLA-A1) complexed with rabbit haemorrhagic disease virus…”. X-ray diffraction at 2.29, 4 pockets (best druggability…
- PDB
- 6M24
- Type
- protein
- Length
- 383 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.29
- Source
- Homo sapiens; Oryctolagus cuniculus; SYNTHETIC CONSTRUCT
- Molecule
- RLA class I histocompatibility antigen, alpha chain 19-1; Beta-2-microglobulin; VP60-2
- UniProt
- P06140, P61769
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · resolution 2.29 · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RLA class I histocompatibility antigen, alpha chain 19-1 | protein | 274 | 28% helix, 40% strand | P06140 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | VP60-2 | protein | 9 | 0% helix, 0% strand | — |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.68 | 0.77 | 56 | empty |
| 2 | 76 | 0.65 | 0.92 | 21 | empty |
| 3 | 109 | 0.41 | 0.76 | 19 | empty |
| 4 | 54 | 0.30 | 0.75 | 12 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1404 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 810 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6M24 · Uncommon structural features of rabbit MHC class I (rla-A1) complexed with rabbit… · the same entry in another collection · chain A against A, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.99
- 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
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 P06140
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6M24 · PDBe 6M24 · UniProt P06140 · UniProt P61769
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