MolNFT v1 · #57011 · protein
Crystal structure of semet-red chlorophyll catabolite reductase
2ZXK · Red chlorophyll catabolite reductase, chloroplastic: “Crystal structure of semet-red chlorophyll catabolite reductase”. X-ray diffraction, 1 ligand (NA), 7 pockets (best druggability 0.84). MolNFT v1 #57011 on GenesisL1: 3D…
- PDB
- 2ZXK
- Type
- protein
- Length
- 519 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
- NA
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Red chlorophyll catabolite reductase, chloroplastic (EC 1.3.1.80) | protein | 266 | 45% helix, 23% strand | Q8LDU4 |
| B | Red chlorophyll catabolite reductase, chloroplastic (EC 1.3.1.80) | protein | 253 | 44% helix, 23% strand | Q8LDU4 |
Ligands and binding sites
- 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 | 452 | 0.84 | 0.92 | 46 | empty |
| 2 | 502 | 0.79 | 0.86 | 51 | empty |
| 3 | 461 | 0.77 | 0.85 | 51 | empty |
| 4 | 115 | 0.56 | 0.84 | 19 | empty |
| 5 | 63 | 0.38 | 0.79 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1161 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 2ZXK · Crystal structure of SeMet-Red chlorophyll catabolite reductase · 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 A against A, TM-score 0.98
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 2ZXK · PDBe 2ZXK · UniProt Q8LDU4
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