MolNFT v1 · #153768 · protein
Crystal structure of pyrrolysyl-tRNA synthetase from methanomethylophilus alvus
6JP2: “Crystal structure of pyrrolysyl-tRNA synthetase from methanomethylophilus alvus”. X-ray diffraction, 15 pockets (best druggability 0.78). MolNFT v1 #153768 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6JP2
- Type
- protein
- Length
- 1,097 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrrolysyl-tRNA synthetase
- EC
- 6.1.1.26
- UniProt
- M9SC49
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrrolysyl-tRNA synthetase (EC 6.1.1.26) | protein | 277 | 38% helix, 22% strand | M9SC49 |
| B | Pyrrolysyl-tRNA synthetase (EC 6.1.1.26) | protein | 272 | 39% helix, 22% strand | M9SC49 |
| C | Pyrrolysyl-tRNA synthetase (EC 6.1.1.26) | protein | 276 | 37% helix, 23% strand | M9SC49 |
| D | Pyrrolysyl-tRNA synthetase (EC 6.1.1.26) | protein | 272 | 37% helix, 21% strand | M9SC49 |
Pockets
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.78 | 0.97 | 35 | empty |
| 2 | 120 | 0.78 | 0.97 | 31 | empty |
| 3 | 689 | 0.72 | 0.78 | 59 | empty |
| 4 | 591 | 0.71 | 0.79 | 58 | empty |
| 5 | 443 | 0.68 | 0.80 | 43 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2336 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 2321 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 555 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 207 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 202 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6JP2 · Crystal structure of pyrrolysyl-tRNA synthetase from Methanomethylophilus alvus · the same entry in another collection · chain A against A, TM-score 1.00
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 M9SC49
- Elsewhere: RCSB PDB 6JP2 · PDBe 6JP2 · UniProt M9SC49
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.