Research workbench
Grie in complex with manganese, succinate and (2S,4R)-5-hydroxyleucine
Analyse Grie in complex with manganese, succinate and (2S,4R)-5-hydroxyleucine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NCJ
- Type
- protein
- Length
- 523 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucine hydroxylase
- UniProt
- A0A0E3URV8
- Ligands
- HL5, MN
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine hydroxylase | protein | 262 | 28% helix, 24% strand | A0A0E3URV8 |
| B | Leucine hydroxylase | protein | 261 | 28% helix, 24% strand | A0A0E3URV8 |
Ligands and binding sites
- HL5 · (2S,4R)-5-hydroxyleucine · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- SIN · Succinic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.79 | 0.98 | 26 | MN, SIN, HL5 |
| 2 | 98 | 0.78 | 0.98 | 25 | MN, SIN, HL5 |
| 3 | 85 | 0.76 | 0.98 | 28 | empty |
| 4 | 310 | 0.56 | 0.76 | 47 | empty |
| 5 | 95 | 0.45 | 0.80 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 932 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5NCJ · GriE in complex with manganese, succinate and (2S,4R)-5-hydroxyleucine · 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 5NCJ · PDBe 5NCJ · UniProt A0A0E3URV8
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