MolNFT v1 · #35741 · protein
Structure of thermus thermophilus proline dehydrogenase inactivated by N-propargylglycine
2EKG · Proline DEHYDROGENASE/DELTA-1-pyrroline-5-carboxylate…: “Structure of thermus thermophilus proline dehydrogenase inactivated by N-propargylglycine”. X-ray diffraction, 1 ligand (FAD), 6 pockets (best druggability 0.70). MolNFT v1…
- PDB
- 2EKG
- Type
- protein
- Length
- 588 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proline DEHYDROGENASE/DELTA-1-pyrroline-5-carboxylate dehydrogenase
- EC
- 1.5.99.8
- UniProt
- Q72IB8
- Ligands
- FAD
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proline DEHYDROGENASE/DELTA-1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.99.8) | protein | 289 | 55% helix, 17% strand | Q72IB8 |
| B | Proline DEHYDROGENASE/DELTA-1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.99.8) | protein | 299 | 55% helix, 16% strand | Q72IB8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 635 | 0.70 | 0.78 | 57 | FAD |
| 2 | 589 | 0.69 | 0.78 | 50 | FAD |
| 3 | 68 | 0.39 | 0.78 | 14 | empty |
| 4 | 77 | 0.38 | 0.77 | 15 | empty |
| 5 | 67 | 0.35 | 0.77 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 999 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor, 2 modified (flavinylation, nonstandard).
Compared structures
- 2EKG · Structure of Thermus thermophilus Proline Dehydrogenase inactivated by N-propargylglycine · the same entry in another collection · chain A against A, TM-score 1.00
- Q72IB8 · AlphaFold monomer V2.0 prediction for proline dehydrogenase (Q72IB8) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q72IB8
- Elsewhere: RCSB PDB 2EKG · PDBe 2EKG · UniProt Q72IB8
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