MolNFT v1 · #67270 · protein
Crystal structure of mtu reca intein, splicing domain
3IFJ · Endonuclease pi-mtui: “Crystal structure of mtu reca intein, splicing domain”. X-ray diffraction, 2 ligands (SNN, ZN), 5 pockets (best druggability 0.76). MolNFT v1 #67270 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3IFJ
- Type
- protein
- Length
- 276 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endonuclease pi-mtui
- EC
- 3.1.-.-
- UniProt
- P0A5U4
- Ligands
- SNN, ZN
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endonuclease pi-mtui (EC 3.1.-.-) | protein | 138 | 7% helix, 58% strand | P0A5U4 |
Ligands and binding sites
- SNN · L-3-aminosuccinimide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.76 | 0.92 | 30 | SNN, ZN |
| 2 | 106 | 0.45 | 0.78 | 25 | empty |
| 3 | 122 | 0.43 | 0.77 | 21 | empty |
| 4 | 100 | 0.43 | 0.78 | 19 | empty |
| 5 | 100 | 0.36 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 781 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3IFJ · Crystal structure of Mtu recA intein, splicing domain · 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 P0A5U4
- Elsewhere: RCSB PDB 3IFJ · PDBe 3IFJ · UniProt P0A5U4
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