MolNFT v1 · #57667 · protein
Structure of the light-independent protochlorophyllide reductase catalyzing a key reduction for greening in the dark
3AEU · Light-independent protochlorophyllide reductase subunit N: “Structure of the light-independent protochlorophyllide reductase catalyzing a key reduction for greening in…”. X-ray diffraction, 1 ligand (SF4), 20 pockets (best…
- PDB
- 3AEU
- Type
- protein
- Length
- 1,664 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light-independent protochlorophyllide reductase subunit N; Light-independent…
- EC
- 1.18.-.-
- UniProt
- P26164, P26163
- Ligands
- SF4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Light-independent protochlorophyllide reductase subunit N (EC 1.18.-.-) | protein | 414 | 50% helix, 17% strand | P26164 |
| B | Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) | protein | 417 | 49% helix, 15% strand | P26163 |
| D | Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) | protein | 419 | 50% helix, 15% strand | P26163 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 347 | 0.82 | 0.92 | 66 | empty |
| 2 | 218 | 0.81 | 0.95 | 38 | empty |
| 3 | 207 | 0.81 | 0.95 | 36 | empty |
| 4 | 69 | 0.76 | 0.99 | 20 | SF4 |
| 5 | 60 | 0.74 | 0.99 | 22 | SF4 |
Interfaces
5 interfaces between chains.
- A–B · 2578 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2515 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 1647 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 839 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 837 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3AEU · Structure of the light-independent protochlorophyllide reductase catalyzing a key… · the same entry in another collection · chain D against D, TM-score 1.00
- P26164 · AlphaFold monomer V2.0 prediction for light-independent protochlorophyllide reductase… · a predicted model of the same protein · chain A against A, TM-score 0.99
- P26163 · AlphaFold monomer V2.0 prediction for light-independent protochlorophyllide reductase… · a predicted model of the same protein · chain B 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 P26164
- Every structure of UniProt P26163
- Elsewhere: RCSB PDB 3AEU · PDBe 3AEU · UniProt P26164 · UniProt P26163
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