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
- 3AES
- Type
- protein
- Length
- 1,670 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 0.86
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 16% 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 | Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) | protein | 420 | 49% helix, 15% strand | P26163 |
| C | Light-independent protochlorophyllide reductase subunit N (EC 1.18.-.-) | protein | 414 | 50% helix, 17% strand | P26164 |
| D | Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) | protein | 421 | 49% 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1132 | 0.86 | 0.86 | 104 | empty |
| 2 | 1064 | 0.85 | 0.85 | 83 | empty |
| 3 | 977 | 0.82 | 0.83 | 67 | empty |
| 4 | 63 | 0.71 | 0.97 | 25 | empty |
| 5 | 452 | 0.65 | 0.78 | 60 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2563 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2522 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 1708 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 842 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 838 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 modified (engineered).
Compared structures
- 3AES · Structure of the light-independent protochlorophyllide reductase catalyzing a key… · the same entry in another collection · chain C against C, TM-score 1.00
- P26164 · AlphaFold monomer V2.0 prediction for light-independent protochlorophyllide reductase… · a predicted model of the same protein · chain C 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 3AES · PDBe 3AES · UniProt P26164 · UniProt P26163
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