Research workbench
Crystal structure of mtu reca intein splicing domain
Analyse Crystal structure of mtu reca intein splicing domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IMZ
- Type
- protein
- Length
- 283 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 0.77
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endonuclease pi-mtui (EC 3.1.-.-) | protein | 143 | 6% helix, 55% strand | P0A5U4 |
| B | Endonuclease pi-mtui (EC 3.1.-.-) | protein | 140 | 6% helix, 59% 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 | 180 | 0.77 | 0.93 | 29 | SNN |
| 2 | 125 | 0.48 | 0.79 | 22 | empty |
| 3 | 122 | 0.45 | 0.77 | 22 | empty |
| 4 | 116 | 0.37 | 0.74 | 20 | empty |
| 5 | 91 | 0.34 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 822 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, oxidation).
Compared structures
- 2IMZ · Crystal structure of Mtu recA intein splicing domain · the same entry in another collection · chain B against B, 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 2IMZ · PDBe 2IMZ · UniProt P0A5U4
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