Research workbench
Crystal structure of rcc-bound red chlorophyll catabolite reductase from arabidopsis thaliana
Analyse Crystal structure of rcc-bound red chlorophyll catabolite reductase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AGA
- Type
- protein
- Length
- 536 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Red chlorophyll catabolite reductase, chloroplastic
- EC
- 1.3.1.80
- UniProt
- Q8LDU4
- Ligands
- RCC, NA
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Red chlorophyll catabolite reductase, chloroplastic (EC 1.3.1.80) | protein | 271 | 45% helix, 21% strand | Q8LDU4 |
| B | Red chlorophyll catabolite reductase, chloroplastic (EC 1.3.1.80) | protein | 265 | 44% helix, 22% strand | Q8LDU4 |
Ligands and binding sites
- RCC · 3-{(2Z,3S,4S)-5-[(Z)-(4-ethenyl-3-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-2-[(5R)-2-[(3-ethyl-5-formyl-4-methyl-1H-pyrrol-2-yl)methyl]-5-(methoxycarbonyl)-3-methyl-4-oxo-4,5-dihydrocyclopenta[b]pyrrol-6(1H)-ylidene]-4-methyl-3,4-dihydro-2H-pyrrol-3-yl}propanoic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 578 | 0.83 | 0.88 | 48 | empty |
| 2 | 507 | 0.79 | 0.86 | 52 | RCC |
| 3 | 590 | 0.78 | 0.83 | 58 | RCC |
| 4 | 112 | 0.50 | 0.81 | 19 | empty |
| 5 | 85 | 0.36 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1113 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3AGA · Crystal structure of RCC-bound red chlorophyll catabolite reductase from Arabidopsis… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8LDU4 · AlphaFold monomer V2.0 prediction for red chlorophyll catabolite reductase, chloroplastic… · a predicted model of the same protein · chain B 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 Q8LDU4
- Elsewhere: RCSB PDB 3AGA · PDBe 3AGA · UniProt Q8LDU4
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