MolNFT v1 · #127976 · protein
Grie in complex with cobalt, alpha-ketoglutarate and L-leucine
5NCI · Leucine hydroxylase: “Grie in complex with cobalt, alpha-ketoglutarate and L-leucine”. X-ray diffraction, 4 ligands (AKG, LEU, CO), 7 pockets (best druggability 0.79). MolNFT v1 #127976 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5NCI
- Type
- protein
- Length
- 526 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucine hydroxylase
- UniProt
- A0A0E3URV8
- Ligands
- AKG, LEU, CO, NA
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine hydroxylase | protein | 262 | 29% helix, 24% strand | A0A0E3URV8 |
| B | Leucine hydroxylase | protein | 264 | 26% helix, 23% strand | A0A0E3URV8 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, B
- LEU · Leucine · ligand · 2 copies · chains A, B
- CO · Cobalt (II) ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.79 | 0.98 | 27 | AKG, LEU |
| 2 | 106 | 0.78 | 0.98 | 25 | CO, AKG, LEU |
| 3 | 89 | 0.76 | 0.97 | 27 | empty |
| 4 | 176 | 0.48 | 0.76 | 26 | empty |
| 5 | 165 | 0.48 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 950 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5NCI · GriE in complex with cobalt, alpha-ketoglutarate and l-leucine · 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 A0A0E3URV8
- Elsewhere: RCSB PDB 5NCI · PDBe 5NCI · UniProt A0A0E3URV8
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