MolNFT v1 · #166713 · protein
Dark-operative protochlorophyllide oxidoreductase in the nucleotide- free form.
6UYK · Light-independent protochlorophyllide reductase iron-sulfur…: “Dark-operative protochlorophyllide oxidoreductase in the nucleotide- free form.”. X-ray diffraction, 2 ligands (SF4, CL), 13 pockets (best druggability 0.79). MolNFT v1…
- PDB
- 6UYK
- Type
- protein
- Length
- 1,040 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein
- EC
- 1.3.7.7
- UniProt
- Q9RFD6
- Ligands
- SF4, CL
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein (EC 1.3.7.7) | protein | 255 | 36% helix, 15% strand | Q9RFD6 |
| B | Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein (EC 1.3.7.7) | protein | 268 | 37% helix, 15% strand | Q9RFD6 |
| C | Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein (EC 1.3.7.7) | protein | 268 | 41% helix, 14% strand | Q9RFD6 |
| D | Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein (EC 1.3.7.7) | protein | 249 | 41% helix, 15% strand | Q9RFD6 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 814 | 0.79 | 0.82 | 87 | empty |
| 2 | 442 | 0.73 | 0.82 | 68 | empty |
| 3 | 79 | 0.41 | 0.78 | 15 | empty |
| 4 | 52 | 0.40 | 0.81 | 12 | empty |
| 5 | 113 | 0.38 | 0.75 | 29 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1410 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1142 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 194 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6UYK · Dark-operative protochlorophyllide oxidoreductase in the nucleotide-free form. · the same entry in another collection · chain D against D, TM-score 1.00
- Q9RFD6 · AlphaFold monomer V2.0 prediction for light-independent protochlorophyllide reductase… · a predicted model of the same protein · chain A against A, TM-score 0.94
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 6UYK · PDBe 6UYK · UniProt Q9RFD6
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