Research workbench
Trans-proline-hydroxylase H11 with succinic and L-proline in the fourth reaction state.
Analyse Trans-proline-hydroxylase H11 with succinic and L-proline in the fourth… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E00
- Type
- protein
- Length
- 530 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phytanoyl-CoA dioxygenase
- UniProt
- S5TUM1
- Ligands
- PRO, AKG, O
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phytanoyl-CoA dioxygenase | protein | 262 | 27% helix, 21% strand | S5TUM1 |
| B | Phytanoyl-CoA dioxygenase | protein | 268 | 27% helix, 24% strand | S5TUM1 |
Ligands and binding sites
- PRO · Proline · ligand · 2 copies · chains A, B
- AKG · 2-oxoglutaric acid · ligand · chains A
- O · Oxygen atom · ion · chains 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
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.76 | 0.99 | 21 | PRO, SIN |
| 2 | 86 | 0.76 | 0.98 | 23 | PRO, SIN |
| 3 | 221 | 0.62 | 0.82 | 27 | empty |
| 4 | 201 | 0.52 | 0.77 | 23 | empty |
| 5 | 140 | 0.47 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 837 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 7E00 · Trans-proline-hydroxylase H11 with Succinic and L-proline in the fourth reaction state. · 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 7E00 · PDBe 7E00 · UniProt S5TUM1
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