Research workbench
Crystal analysis of DELTA1-pyrroline-5-carboxylate dehydrogenase from thermus thermophilus with bound L-alanine
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
- 2EJD
- 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
- ALA, NA
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12) | protein | 516 | 41% helix, 21% strand | Q5SI02 |
Ligands and binding sites
- ALA · Alanine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 13 copies · chains A, B
- ACT · Acetate ion · additive · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 640 | 0.81 | 0.86 | 61 | MPD |
| 2 | 345 | 0.72 | 0.84 | 66 | ALA, MPD |
| 3 | 363 | 0.69 | 0.82 | 66 | ALA, MPD |
| 4 | 515 | 0.69 | 0.79 | 46 | MPD |
| 5 | 471 | 0.68 | 0.79 | 41 | MPD |
Interfaces
1 interface between chains.
- A–B · 3133 Ų buried · 56 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 2EJD · Crystal analysis of delta1-pyrroline-5-carboxylate dehydrogenase from Thermus… · 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 Q5SI02
- Elsewhere: RCSB PDB 2EJD · PDBe 2EJD · UniProt Q5SI02
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