MolNFT v1 · #141026 · protein
Structural basis for recognition of L-lysine, L-ornithine, and L-2,4- diamino butyric acid by lysine cyclodeaminase
5YU1: “Structural basis for recognition of L-lysine, L-ornithine, and L-2,4- diamino butyric acid by lysine…”. X-ray diffraction, 3 ligands (NAD, YCP, NA), 9 pockets (best druggability 0.78). MolNFT v1 #141026 on GenesisL1: 3D structure…
- PDB
- 5YU1
- Type
- protein
- Length
- 1,376 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine cyclodeaminase
- EC
- 4.3.1.12
- UniProt
- D9UBW0
- Ligands
- NAD, YCP, NA
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Lysine cyclodeaminase (EC 4.3.1.12) | protein | 344 | 40% helix, 22% strand | D9UBW0 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- YCP · (2S)-piperidine-2-carboxylic acid · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 322 | 0.78 | 0.89 | 48 | NAD, YCP |
| 2 | 313 | 0.78 | 0.89 | 50 | NAD, YCP |
| 3 | 322 | 0.77 | 0.89 | 51 | NAD, YCP |
| 4 | 312 | 0.77 | 0.89 | 48 | NAD, YCP |
| 5 | 479 | 0.67 | 0.79 | 57 | empty |
Interfaces
4 interfaces between chains.
- A–B · 3231 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 3227 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 759 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 35 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5YU1 · Structural basis for recognition of L-lysine, L-ornithine, and L-2,4-diamino butyric acid… · 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 5YU1 · PDBe 5YU1 · UniProt D9UBW0
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