MolNFT v1 · #155250 · protein
Crystal structure of light-dependent protochlorophyllide oxidoreductase from thermosynechococcus elongatus
6L1H · NADPH-protochlorophyllide oxidoreductase: “Crystal structure of light-dependent protochlorophyllide oxidoreductase from thermosynechococcus elongatus”. X-ray diffraction, 1 ligand (NDP), 5 pockets (best druggability 0.78). MolNFT v1…
- PDB
- 6L1H
- Type
- protein
- Length
- 606 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADPH-protochlorophyllide oxidoreductase
- EC
- 1.3.1.33
- UniProt
- Q8DLC1
- Ligands
- NDP
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADPH-protochlorophyllide oxidoreductase (EC 1.3.1.33) | protein | 301 | 49% helix, 15% strand | Q8DLC1 |
| B | NADPH-protochlorophyllide oxidoreductase (EC 1.3.1.33) | protein | 305 | 47% helix, 15% strand | Q8DLC1 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 434 | 0.78 | 0.86 | 50 | NDP |
| 2 | 397 | 0.78 | 0.87 | 48 | NDP |
| 3 | 216 | 0.55 | 0.79 | 32 | empty |
| 4 | 142 | 0.45 | 0.76 | 18 | empty |
| 5 | 72 | 0.34 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 870 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6L1H · Crystal structure of light-dependent protochlorophyllide oxidoreductase from… · 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 Q8DLC1
- Elsewhere: RCSB PDB 6L1H · PDBe 6L1H · UniProt Q8DLC1
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