MolNFT v1 · #137762 · protein
Crystal structure of the photosynthetic phosphoenolpyruvate carboxylase isoenzyme from maize in complex with gly
5VYJ: “Crystal structure of the photosynthetic phosphoenolpyruvate carboxylase isoenzyme from maize in complex with…”. X-ray diffraction, 1 ligand (GLY), 20 pockets (best druggability 0.85). MolNFT v1 #137762 on GenesisL1: 3D structure…
- PDB
- 5VYJ
- Type
- protein
- Length
- 3,671 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoenolpyruvate carboxylase
- EC
- 4.1.1.31
- UniProt
- Q84KR7
- Ligands
- GLY
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 64% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoenolpyruvate carboxylase (EC 4.1.1.31) | protein | 918 | 64% helix, 6% strand | Q84KR7 |
| B | Phosphoenolpyruvate carboxylase (EC 4.1.1.31) | protein | 917 | 63% helix, 6% strand | Q84KR7 |
| C | Phosphoenolpyruvate carboxylase (EC 4.1.1.31) | protein | 918 | 63% helix, 6% strand | Q84KR7 |
| D | Phosphoenolpyruvate carboxylase (EC 4.1.1.31) | protein | 918 | 65% helix, 6% strand | Q84KR7 |
Ligands and binding sites
- GLY · Glycine · ligand · 5 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 13 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 910 | 0.85 | 0.87 | 87 | empty |
| 2 | 804 | 0.84 | 0.87 | 76 | empty |
| 3 | 1039 | 0.84 | 0.85 | 99 | empty |
| 4 | 994 | 0.84 | 0.85 | 88 | empty |
| 5 | 940 | 0.77 | 0.79 | 64 | ACT |
Interfaces
4 interfaces between chains.
- C–D · 2471 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 2429 Ų buried · 52 hydrogen bonds · protein-protein
- B–D · 629 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 624 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5VYJ · Crystal structure of the photosynthetic phosphoenolpyruvate carboxylase isoenzyme from… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q84KR7
- Elsewhere: RCSB PDB 5VYJ · PDBe 5VYJ · UniProt Q84KR7
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