MolNFT v1 · #153078 · protein
Crystal structure of bat (pteropus alecto) MHC class I ptal-N*01:01 in complex with MERS-cov-derived peptide MERS-cov-S3
6J2J: “Crystal structure of bat (pteropus alecto) MHC class I ptal-N*01:01 in complex with MERS-cov-derived peptide…”. X-ray diffraction, 10 pockets (best druggability 0.76). MolNFT v1 #153078 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6J2J
- Type
- protein
- Length
- 758 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ptal-N*01:01; Beta-2-microglobulin; MERS-cov-S3
- UniProt
- A0A125R585, P61769
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Ptal-N*01:01 | protein | 277 | 27% helix, 39% strand | A0A125R585 |
| B, E | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C, F | MERS-cov-S3 | protein | 3 | 0% helix, 0% strand | — |
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 917 | 0.76 | 0.79 | 70 | empty |
| 2 | 462 | 0.69 | 0.80 | 48 | empty |
| 3 | 388 | 0.69 | 0.81 | 40 | empty |
| 4 | 243 | 0.57 | 0.78 | 24 | empty |
| 5 | 102 | 0.47 | 0.80 | 19 | empty |
Interfaces
7 interfaces between chains.
- D–E · 1343 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1331 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 517 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 517 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 296 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6J2J · Crystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:01 in complex with… · 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 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 A0A125R585
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6J2J · PDBe 6J2J · UniProt A0A125R585 · UniProt P61769
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