Research workbench
Structure of the light-independent protochlorophyllide reductase catalyzing a key reduction for greening in the dark
Analyse Structure of the light-independent protochlorophyllide reductase catalyzing a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AEQ
- Type
- protein
- Length
- 1,667 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- Rhodobacter capsulatus
- Molecule
- Light-independent protochlorophyllide reductase subunit N; Light-independent…
- EC
- 1.18.-.-
- UniProt
- P26164, P26163
- Ligands
- SF4, PMR
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · resolution 2.9 · 3 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Light-independent protochlorophyllide reductase subunit N (EC 1.18.-.-) | protein | 415 | 48% helix, 17% strand | P26164 |
| B, D | Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) | protein | 419 | 46% helix, 16% strand | P26163 |
| C | Light-independent protochlorophyllide reductase subunit N (EC 1.18.-.-) | protein | 414 | 49% helix, 17% strand | P26164 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B, C, D
- PMR · Protochlorophyllide · ligand · 2 copies · chains B, C, D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 640 | 0.88 | 0.92 | 74 | PMR |
| 2 | 657 | 0.88 | 0.92 | 64 | PMR |
| 3 | 502 | 0.81 | 0.88 | 63 | empty |
| 4 | 55 | 0.70 | 0.97 | 19 | empty |
| 5 | 466 | 0.63 | 0.77 | 69 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2511 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2489 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 1408 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1007 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 984 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3AEQ · 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 0.99
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 P26164
- Every structure of UniProt P26163
- Elsewhere: RCSB PDB 3AEQ · PDBe 3AEQ · UniProt P26164 · UniProt P26163
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