MolNFT v1 · #73820 · protein
Archaeal-type phosphoenolpyruvate carboxylase
3ODM: “Archaeal-type phosphoenolpyruvate carboxylase”. X-ray diffraction, 1 ligand (AUC), 20 pockets (best druggability 0.74). MolNFT v1 #73820 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3ODM
- Type
- protein
- Length
- 4,217 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoenolpyruvate carboxylase
- EC
- 4.1.1.31
- UniProt
- Q8XLE8
- Ligands
- AUC
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 7 distinct chains · 57% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoenolpyruvate carboxylase (EC 4.1.1.31) | protein | 525 | 57% helix, 9% strand | Q8XLE8 |
| B, F | Phosphoenolpyruvate carboxylase (EC 4.1.1.31) | protein | 529 | 57% helix, 9% strand | Q8XLE8 |
| C | Phosphoenolpyruvate carboxylase (EC 4.1.1.31) | protein | 530 | 55% helix, 8% strand | Q8XLE8 |
| D | Phosphoenolpyruvate carboxylase (EC 4.1.1.31) | protein | 526 | 58% helix, 8% strand | Q8XLE8 |
| E | Phosphoenolpyruvate carboxylase (EC 4.1.1.31) | protein | 524 | 59% helix, 9% strand | Q8XLE8 |
| G | Phosphoenolpyruvate carboxylase (EC 4.1.1.31) | protein | 527 | 56% helix, 8% strand | Q8XLE8 |
| H | Phosphoenolpyruvate carboxylase (EC 4.1.1.31) | protein | 527 | 57% helix, 9% strand | Q8XLE8 |
Ligands and binding sites
- AUC · Gold (I) cyanide ion · ligand · 36 copies · chains A, B, H, C, D, E, F, G
- MLI · Malonate ion · additive · 5 copies · chains A, C, D, E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 530 | 0.74 | 0.82 | 61 | AUC, MLI |
| 2 | 119 | 0.73 | 0.93 | 30 | AUC, MLI |
| 3 | 75 | 0.72 | 0.97 | 28 | AUC, MLI |
| 4 | 420 | 0.72 | 0.83 | 56 | AUC |
| 5 | 511 | 0.70 | 0.80 | 60 | AUC |
Interfaces
14 interfaces between chains.
- F–G · 1224 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1221 Ų buried · 13 hydrogen bonds · protein-protein
- B–H · 1215 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 1182 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 714 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
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 Q8XLE8
- Elsewhere: RCSB PDB 3ODM · PDBe 3ODM · UniProt Q8XLE8
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