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Crystal structure of light-dependent protochlorophyllide oxidoreductase from synechocystis sp. pcc 6803
Analyse Crystal structure of light-dependent protochlorophyllide oxidoreductase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L1G
- Type
- protein
- Length
- 594 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light-dependent protochlorophyllide reductase
- EC
- 1.3.1.33
- UniProt
- Q59987
- Ligands
- NDP, SO4
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Light-dependent protochlorophyllide reductase (EC 1.3.1.33) | protein | 301 | 46% helix, 15% strand | Q59987 |
| B | Light-dependent protochlorophyllide reductase (EC 1.3.1.33) | protein | 293 | 46% helix, 15% strand | Q59987 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 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 | 517 | 0.77 | 0.84 | 66 | NDP |
| 2 | 533 | 0.75 | 0.82 | 57 | NDP |
| 3 | 201 | 0.56 | 0.79 | 26 | empty |
| 4 | 210 | 0.49 | 0.75 | 28 | empty |
| 5 | 50 | 0.29 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 734 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6L1G · Crystal structure of light-dependent protochlorophyllide oxidoreductase from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q59987 · AlphaFold monomer V2.0 prediction for light-dependent protochlorophyllide reductase… · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q59987
- Elsewhere: RCSB PDB 6L1G · PDBe 6L1G · UniProt Q59987
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