MolNFT v1 · #153076 · protein
Crystal structure of bat (pteropus alecto) MHC class I ptal-N*01:01 mutant (MET52 ASP53 LEU54 deleted) in complex with hendra virus- derived peptide HEV1
6J2H · Ptal-N*01:01 (MET52 ASP53 LEU54 deleted): “Crystal structure of bat (pteropus alecto) MHC class I ptal-N*01:01 mutant (MET52 ASP53 LEU54 deleted) in…”. X-ray diffraction, 7 pockets (best druggability 0.75). MolNFT v1 #153076 on…
- PDB
- 6J2H
- Type
- protein
- Length
- 764 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ptal-N*01:01 (MET52 ASP53 LEU54 deleted); Beta-2-microglobulin; HEV1
- UniProt
- A0A125R585, P61769
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Ptal-N*01:01 (MET52 ASP53 LEU54 deleted) | protein | 273 | 27% helix, 40% strand | A0A125R585 |
| B, E | Beta-2-microglobulin | protein | 101 | 0% helix, 49% strand | P61769 |
| C, F | HEV1 | protein | 8 | 0% helix, 0% strand | — |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.75 | 0.77 | 90 | empty |
| 2 | 575 | 0.69 | 0.78 | 52 | empty |
| 3 | 454 | 0.68 | 0.80 | 47 | empty |
| 4 | 94 | 0.44 | 0.79 | 20 | empty |
| 5 | 94 | 0.42 | 0.79 | 19 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1509 Ų buried · 26 hydrogen bonds · protein-protein
- D–E · 1436 Ų buried · 24 hydrogen bonds · protein-protein
- D–F · 910 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 891 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 311 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6J2H · Crystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:01 mutant (Met52 Asp53… · 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 6J2H · PDBe 6J2H · UniProt A0A125R585 · UniProt P61769
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