MolNFT v1 · #153073 · protein
Crystal structure of bat (pteropus alecto) MHC class I ptal-N*01:01 in complex with ebola virus-derived peptide ebov-NP1
6J2E · MHC class I antigen: “Crystal structure of bat (pteropus alecto) MHC class I ptal-N*01:01 in complex with ebola virus-derived…”. X-ray diffraction, 6 pockets (best druggability 0.77). MolNFT v1 #153073 on GenesisL1: 3D structure…
- PDB
- 6J2E
- Type
- protein
- Length
- 772 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Ebov-NP1
- UniProt
- A0A125R585, P61769
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | MHC class I antigen | protein | 277 | 26% helix, 41% strand | A0A125R585 |
| B, E | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C, F | Ebov-NP1 | protein | 10 | 0% helix, 0% strand | — |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 930 | 0.77 | 0.80 | 91 | empty |
| 2 | 504 | 0.68 | 0.79 | 51 | empty |
| 3 | 348 | 0.68 | 0.82 | 37 | empty |
| 4 | 104 | 0.44 | 0.78 | 16 | empty |
| 5 | 81 | 0.41 | 0.79 | 17 | empty |
Interfaces
7 interfaces between chains.
- D–E · 1380 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1336 Ų buried · 23 hydrogen bonds · protein-protein
- D–F · 988 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 986 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 317 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6J2E · Crystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:01 in complex with Ebola… · the same entry in another collection · chain F against F, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain E 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 A0A125R585
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6J2E · PDBe 6J2E · UniProt A0A125R585 · UniProt P61769
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