MolNFT v1 · #34946 · protein
Crystal structure of restriction endonucleases pabi
2DVY · Restriction endonuclease pabi: “Crystal structure of restriction endonucleases pabi”. X-ray diffraction, 17 pockets (best druggability 0.85). MolNFT v1 #34946 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2DVY
- Type
- protein
- Length
- 1,304 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Restriction endonuclease pabi
- UniProt
- Q9V2B6
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Restriction endonuclease pabi | protein | 223 | 26% helix, 30% strand | Q9V2B6 |
| B | Restriction endonuclease pabi | protein | 215 | 27% helix, 27% strand | Q9V2B6 |
| C | Restriction endonuclease pabi | protein | 218 | 28% helix, 31% strand | Q9V2B6 |
| D | Restriction endonuclease pabi | protein | 214 | 21% helix, 29% strand | Q9V2B6 |
| F | Restriction endonuclease pabi | protein | 211 | 26% helix, 27% strand | Q9V2B6 |
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 997 | 0.85 | 0.86 | 116 | empty |
| 2 | 739 | 0.82 | 0.86 | 66 | empty |
| 3 | 301 | 0.77 | 0.89 | 39 | empty |
| 4 | 831 | 0.76 | 0.80 | 85 | empty |
| 5 | 423 | 0.74 | 0.84 | 36 | empty |
Interfaces
11 interfaces between chains.
- E–F · 1711 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1703 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1700 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 926 Ų buried · 13 hydrogen bonds · protein-protein
- C–F · 912 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 2DVY · Crystal structure of restriction endonucleases PabI · 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 Q9V2B6
- Elsewhere: RCSB PDB 2DVY · PDBe 2DVY · UniProt Q9V2B6
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