Research workbench
Crystal structure of DELTA1-piperideine-2-carboxylate reductase from pseudomonas syringae complexed with NADPH and pyrrole-2-carboxylate
Analyse Crystal structure of DELTA1-piperideine-2-carboxylate reductase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CWH
- Type
- protein
- Length
- 669 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DELTA1-piperideine-2-carboxylate reductase
- EC
- 1.5.1.-
- UniProt
- Q4U331
- Ligands
- NDP, PYC
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DELTA1-piperideine-2-carboxylate reductase (EC 1.5.1.-) | protein | 332 | 43% helix, 20% strand | Q4U331 |
| B | DELTA1-piperideine-2-carboxylate reductase (EC 1.5.1.-) | protein | 337 | 42% helix, 20% strand | Q4U331 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- PYC · Pyrrole-2-carboxylate · ligand · 2 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 | 541 | 0.76 | 0.83 | 55 | NDP, PYC |
| 2 | 562 | 0.75 | 0.82 | 60 | NDP, PYC |
| 3 | 149 | 0.48 | 0.78 | 18 | empty |
| 4 | 178 | 0.46 | 0.75 | 30 | empty |
| 5 | 82 | 0.44 | 0.80 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2817 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 2CWH · Crystal Structure of delta1-piperideine-2-carboxylate reductase from Pseudomonas syringae… · the same entry in another collection · chain A against A, TM-score 1.00
- Q4U331 · AlphaFold monomer V2.0 prediction for DELTA(1)-pyrroline-2-CARBOXYLATE/DELTA(1)-piperidein… · 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 Q4U331
- Elsewhere: RCSB PDB 2CWH · PDBe 2CWH · UniProt Q4U331
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