Research workbench
Trans-3/4-proline-hydroxylase H11 with akg and L-proline
Analyse Trans-3/4-proline-hydroxylase H11 with akg and L-proline in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E07
- Type
- protein
- Length
- 535 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phytanoyl-CoA dioxygenase
- UniProt
- S5TUM1
- Ligands
- AKG, PRO, FE
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phytanoyl-CoA dioxygenase | protein | 267 | 27% helix, 21% strand | S5TUM1 |
| B | Phytanoyl-CoA dioxygenase | protein | 268 | 27% helix, 21% strand | S5TUM1 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, B
- PRO · Proline · ligand · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.78 | 0.98 | 27 | AKG, PRO |
| 2 | 85 | 0.76 | 0.98 | 23 | FE, AKG, PRO |
| 3 | 237 | 0.65 | 0.83 | 28 | empty |
| 4 | 160 | 0.48 | 0.77 | 25 | empty |
| 5 | 153 | 0.46 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 898 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 7E07 · Trans-3/4-proline-hydroxylase H11 with AKG and L-proline · 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 S5TUM1
- Elsewhere: RCSB PDB 7E07 · PDBe 7E07 · UniProt S5TUM1
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