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
- 3ZGB
- Type
- protein
- Length
- 1,835 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoenolpyruvate carboxylase
- EC
- 4.1.1.31
- UniProt
- Q01647
- Ligands
- ASP, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 65% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoenolpyruvate carboxylase (EC 4.1.1.31) | protein | 920 | 65% helix, 6% strand | Q01647 |
| B | Phosphoenolpyruvate carboxylase (EC 4.1.1.31) | protein | 915 | 65% helix, 6% strand | Q01647 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.83 | 0.93 | 51 | SO4 |
| 2 | 273 | 0.83 | 0.94 | 39 | SO4 |
| 3 | 921 | 0.81 | 0.83 | 95 | empty |
| 4 | 578 | 0.81 | 0.86 | 52 | empty |
| 5 | 566 | 0.79 | 0.85 | 52 | empty |
Interfaces
1 interface between chains.
- A–B · 809 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- Q01647 · AlphaFold monomer V2.0 prediction for phosphoenolpyruvate carboxylase (Q01647) · 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 Q01647
- Elsewhere: RCSB PDB 3ZGB · PDBe 3ZGB · UniProt Q01647
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