Research workbench
Crystal structure of the aperopyrum pernix RNA splicing endonuclease
Analyse Crystal structure of the aperopyrum pernix RNA splicing endonuclease in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P1Z
- Type
- protein
- Length
- 2,079 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein; TRNA-splicing endonuclease
- EC
- 3.1.27.9
- UniProt
- Q9YE85, Q9YBF1
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I | Putative uncharacterized protein | protein | 168 | 33% helix, 32% strand | Q9YE85 |
| B, F, J | TRNA-splicing endonuclease (EC 3.1.27.9) | protein | 180 | 31% helix, 29% strand | Q9YBF1 |
| C, G, K | Putative uncharacterized protein | protein | 161 | 34% helix, 34% strand | Q9YE85 |
| D, H, L | TRNA-splicing endonuclease (EC 3.1.27.9) | protein | 184 | 30% helix, 31% strand | Q9YBF1 |
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 912 | 0.79 | 0.81 | 71 | empty |
| 2 | 1064 | 0.75 | 0.78 | 102 | empty |
| 3 | 557 | 0.72 | 0.81 | 54 | empty |
| 4 | 579 | 0.71 | 0.79 | 61 | empty |
| 5 | 537 | 0.70 | 0.80 | 60 | empty |
Interfaces
20 interfaces between chains.
- C–D · 1582 Ų buried · 27 hydrogen bonds · protein-protein
- I–J · 1566 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1554 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1549 Ų buried · 25 hydrogen bonds · protein-protein
- G–H · 1544 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 3P1Z · Crystal structure of the Aperopyrum pernix RNA splicing endonuclease · the same entry in another collection · chain L against L, 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 Q9YE85
- Every structure of UniProt Q9YBF1
- Elsewhere: RCSB PDB 3P1Z · PDBe 3P1Z · UniProt Q9YE85 · UniProt Q9YBF1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.