Research workbench
Uncommon structural features of rabbit MHC class I (rla-A1) complexed with rabbit haemorrhagic disease virus (rhdv) derived peptide, VP60-1
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
- 6M2J
- Type
- protein
- Length
- 383 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rla class I histocompatibility antigen, alpha chain 19-1; Beta-2-microglobulin; VP60-1
- UniProt
- P06140, P61769
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 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 | VP60-1 | protein | 9 | 0% helix, 0% strand | — |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 595 | 0.67 | 0.77 | 54 | empty |
| 2 | 66 | 0.35 | 0.77 | 18 | empty |
| 3 | 57 | 0.29 | 0.74 | 15 | empty |
| 4 | 55 | 0.29 | 0.74 | 11 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1414 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 930 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6M2J · 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 0.97
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 6M2J · PDBe 6M2J · UniProt P06140 · UniProt P61769
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