Research workbench
Crystal structure of the omega transaminase from chromobacterium violaceum in the apo form, crystallised from peg 3350
Analyse Crystal structure of the omega transaminase from chromobacterium violaceum in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A6U
- Type
- protein
- Length
- 778 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Omega transaminase
- EC
- 2.6.1.18, 2.6.1.62
- UniProt
- Q7NWG4
- Ligands
- NA, SCN
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Omega transaminase (EC 2.6.1.18, 2.6.1.62) | protein | 389 | 45% helix, 20% strand | Q7NWG4 |
| B | Omega transaminase (EC 2.6.1.18, 2.6.1.62) | protein | 389 | 44% helix, 19% strand | Q7NWG4 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- SCN · Thiocyanate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 664 | 0.72 | 0.79 | 70 | SCN |
| 2 | 618 | 0.69 | 0.78 | 69 | empty |
| 3 | 64 | 0.34 | 0.76 | 15 | empty |
| 4 | 54 | 0.34 | 0.77 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 2001 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 4A6U · Crystal structure of the omega transaminase from Chromobacterium violaceum in the apo… · 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 Q7NWG4
- Elsewhere: RCSB PDB 4A6U · PDBe 4A6U · UniProt Q7NWG4
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