MolNFT v1 · #40793 · protein
1-pyrroline-5-carboxylate dehydrogenase from thermus thermophilus with bound inhibitor L-proline and NAD.
2J40: “1-pyrroline-5-carboxylate dehydrogenase from thermus thermophilus with bound inhibitor L-proline and NAD.”. X-ray diffraction, 3 ligands (PRO, NAD, NA), 7 pockets (best druggability 0.81). MolNFT v1 #40793 on GenesisL1: 3D…
- PDB
- 2J40
- 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
- PRO, NAD, NA
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 41% 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 | 41% helix, 20% strand | Q5SI02 |
Ligands and binding sites
- PRO · Proline · 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
- ACT · Acetate ion · additive · 4 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, B
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.81 | 0.86 | 67 | empty |
| 2 | 774 | 0.76 | 0.80 | 94 | PRO, NAD, ACT, MRD |
| 3 | 720 | 0.75 | 0.80 | 99 | PRO, NAD, ACT |
| 4 | 404 | 0.65 | 0.79 | 41 | ACT |
| 5 | 425 | 0.65 | 0.78 | 38 | ACT |
Interfaces
1 interface between chains.
- A–B · 3162 Ų buried · 57 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 2J40 · 1-pyrroline-5-carboxylate dehydrogenase from Thermus thermophilus with bound inhibitor… · 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 2J40 · PDBe 2J40 · UniProt Q5SI02
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