Research workbench
CYCLODEAMINASE_PA
Analyse CYCLODEAMINASE_PA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GZJ
- Type
- protein
- Length
- 701 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine cyclodeaminase
- EC
- 4.3.1.12
- UniProt
- D9UBW0
- Ligands
- NAD
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine cyclodeaminase (EC 4.3.1.12) | protein | 348 | 38% helix, 22% strand | D9UBW0 |
| B | Lysine cyclodeaminase (EC 4.3.1.12) | protein | 353 | 39% helix, 22% strand | D9UBW0 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.80 | 0.90 | 54 | NAD |
| 2 | 340 | 0.77 | 0.88 | 54 | NAD |
Interfaces
1 interface between chains.
- A–B · 3370 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 5GZJ · Cyclodeaminase_PA · 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 D9UBW0
- Elsewhere: RCSB PDB 5GZJ · PDBe 5GZJ · UniProt D9UBW0
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