Research workbench
Greater efficiency of photosynthetic carbon fixation due to single amino acid substitution
Analyse Greater efficiency of photosynthetic carbon fixation due to single amino acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZGE
- Type
- protein
- Length
- 1,827 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C4 phosphoenolpyruvate carboxylase
- EC
- 4.1.1.31
- UniProt
- P30694
- Ligands
- ASP, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C4 phosphoenolpyruvate carboxylase (EC 4.1.1.31) | protein | 916 | 66% helix, 5% strand | P30694 |
| B | C4 phosphoenolpyruvate carboxylase (EC 4.1.1.31) | protein | 911 | 66% helix, 5% strand | P30694 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1051 | 0.84 | 0.85 | 96 | empty |
| 2 | 725 | 0.81 | 0.85 | 80 | empty |
| 3 | 446 | 0.79 | 0.87 | 49 | empty |
| 4 | 267 | 0.78 | 0.91 | 42 | ASP |
| 5 | 282 | 0.77 | 0.89 | 43 | ASP |
Interfaces
1 interface between chains.
- A–B · 687 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3ZGE · Greater efficiency of photosynthetic carbon fixation due to single amino acid substitution · the same entry in another collection · chain B against B, TM-score 1.00
- P30694 · AlphaFold monomer V2.0 prediction for C4 phosphoenolpyruvate carboxylase (P30694) · a predicted model of the same protein · chain A 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 P30694
- Elsewhere: RCSB PDB 3ZGE · PDBe 3ZGE · UniProt P30694
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