Research workbench
Crystal structure of the L protein of rhodobacter sphaeroides light- independent protochlorophyllide reductase (bchl) with mgadp bound: a homologue of the nitrogenase fe protein
Analyse Crystal structure of the L protein of rhodobacter sphaeroides light… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FWY
- Type
- protein
- Length
- 536 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein
- EC
- 1.18.-.-
- UniProt
- Q9RFD6
- Ligands
- ADP, SF4, MG
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein (EC 1.18.-.-) | protein | 268 | 43% helix, 16% strand | Q9RFD6 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- SF4 · Iron/sulfur cluster · ligand · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 761 | 0.80 | 0.84 | 94 | MG, ADP |
| 2 | 272 | 0.74 | 0.87 | 51 | empty |
| 3 | 92 | 0.42 | 0.79 | 19 | empty |
| 4 | 76 | 0.39 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1534 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3FWY · Crystal structure of the L protein of Rhodobacter sphaeroides light-independent… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9RFD6 · AlphaFold monomer V2.0 prediction for light-independent protochlorophyllide reductase… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q9RFD6
- Elsewhere: RCSB PDB 3FWY · PDBe 3FWY · UniProt Q9RFD6
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