MolNFT v1 · #32814 · protein
Structure of the bfii restriction endonuclease
2C1L: “Structure of the bfii restriction endonuclease”. X-ray diffraction, 2 ligands (SRT, BCT), 7 pockets (best druggability 0.78). MolNFT v1 #32814 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2C1L
- Type
- protein
- Length
- 716 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Restriction endonuclease
- EC
- 3.1.21.4
- UniProt
- Q9F4C9
- Ligands
- SRT, BCT
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Restriction endonuclease (EC 3.1.21.4) | protein | 358 | 25% helix, 32% strand | Q9F4C9 |
Ligands and binding sites
- SRT · S,R meso-tartaric acid · ligand · 2 copies · chains A, B
- BCT · Bicarbonate ion · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B
- TAR · D(-)-tartaric acid · additive · chains A
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 | 1146 | 0.78 | 0.80 | 77 | TLA, MES, SRT |
| 2 | 684 | 0.74 | 0.80 | 61 | TRS |
| 3 | 381 | 0.71 | 0.82 | 38 | empty |
| 4 | 200 | 0.57 | 0.80 | 26 | empty |
| 5 | 101 | 0.37 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2313 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 2C1L · Structure of the BfiI restriction endonuclease · 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 Q9F4C9
- Elsewhere: RCSB PDB 2C1L · PDBe 2C1L · UniProt Q9F4C9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.