Research workbench
Crystal analysis of DELTA1-pyrroline-5-carboxylate dehydrogenase from thermus thermophilus with bound L-valine and NAD.
Analyse Crystal analysis of DELTA1-pyrroline-5-carboxylate dehydrogenase from thermus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EII
- Type
- protein
- Length
- 1,032 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1-pyrroline-5-carboxylate dehydrogenase
- EC
- 1.5.1.12
- UniProt
- Q5SI02
- Ligands
- VAL, NAD, NA
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12) | protein | 516 | 42% helix, 20% strand | Q5SI02 |
Ligands and binding sites
- VAL · Valine · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 14 copies · chains A, B
- ACT · Acetate ion · additive · 4 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 590 | 0.80 | 0.86 | 58 | MPD |
| 2 | 815 | 0.77 | 0.80 | 99 | ACT, VAL, NAD, MPD |
| 3 | 341 | 0.70 | 0.83 | 62 | VAL, MPD |
| 4 | 462 | 0.66 | 0.78 | 41 | ACT, MPD |
| 5 | 411 | 0.65 | 0.78 | 37 | ACT, MPD |
Interfaces
1 interface between chains.
- A–B · 3149 Ų buried · 55 hydrogen bonds · protein-protein
Compared structures
- 2EII · Crystal analysis of delta1-pyrroline-5-carboxylate dehydrogenase from Thermus… · the same entry in another collection · chain B against B, 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 Q5SI02
- Elsewhere: RCSB PDB 2EII · PDBe 2EII · UniProt Q5SI02
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