MolNFT v1 · #57825 · protein
Splicing endonuclease from aeropyrum pernix
3AJV · Putative uncharacterized protein: “Splicing endonuclease from aeropyrum pernix”. X-ray diffraction, 1 ligand (CL), 7 pockets (best druggability 0.68). MolNFT v1 #57825 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3AJV
- Type
- protein
- Length
- 687 residues
- Chains
- 4
- 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
- Ligands
- CL
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uncharacterized protein | protein | 168 | 33% helix, 33% strand | Q9YE85 |
| B | TRNA-splicing endonuclease (EC 3.1.27.9) | protein | 180 | 31% helix, 31% strand | Q9YBF1 |
| C | Putative uncharacterized protein | protein | 161 | 34% helix, 34% strand | Q9YE85 |
| D | TRNA-splicing endonuclease (EC 3.1.27.9) | protein | 178 | 31% helix, 31% strand | Q9YBF1 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains B, C, A, D
- GOL · Glycerol · additive · 10 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 469 | 0.68 | 0.79 | 55 | GOL |
| 2 | 319 | 0.61 | 0.78 | 36 | GOL |
| 3 | 200 | 0.57 | 0.80 | 27 | GOL |
| 4 | 138 | 0.53 | 0.80 | 19 | GOL |
| 5 | 152 | 0.42 | 0.74 | 28 | GOL |
Interfaces
5 interfaces between chains.
- C–D · 1536 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1531 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 1011 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 1000 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 627 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
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 3AJV · PDBe 3AJV · UniProt Q9YE85 · UniProt Q9YBF1
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