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Pyruvate decarboxylase variant GLU473ASP from Z. mobilis in complex with reaction intermediate 2-lactyl-thdp
Analyse Pyruvate decarboxylase variant GLU473ASP from Z. mobilis in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OE1
- Type
- protein
- Length
- 2,245 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate decarboxylase
- EC
- 4.1.1.1
- UniProt
- P06672
- Ligands
- TDL, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Pyruvate decarboxylase (EC 4.1.1.1) | protein | 565 | 41% helix, 19% strand | P06672 |
| B | Pyruvate decarboxylase (EC 4.1.1.1) | protein | 560 | 41% helix, 19% strand | P06672 |
| D | Pyruvate decarboxylase (EC 4.1.1.1) | protein | 555 | 40% helix, 19% strand | P06672 |
Ligands and binding sites
- TDL · 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-(1-carboxy-1-hydroxyethyl)-5-(2-{[hydroxy(phosphonooxy) phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 534 | 0.83 | 0.89 | 81 | empty |
| 2 | 160 | 0.81 | 0.97 | 48 | TDL |
| 3 | 144 | 0.81 | 0.98 | 42 | MG, TDL |
| 4 | 152 | 0.80 | 0.97 | 40 | TDL |
| 5 | 154 | 0.80 | 0.96 | 43 | MG, TDL |
Interfaces
6 interfaces between chains.
- A–B · 4284 Ų buried · 72 hydrogen bonds · protein-protein
- C–D · 4215 Ų buried · 84 hydrogen bonds · protein-protein
- A–D · 1305 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1295 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 773 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3OE1 · Pyruvate decarboxylase variant Glu473Asp from Z. mobilis in complex with reaction… · the same entry in another collection · chain A against A, TM-score 1.00
- P06672 · AlphaFold monomer V2.0 prediction for pyruvate decarboxylase (P06672) · a predicted model of the same protein · chain D 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 P06672
- Elsewhere: RCSB PDB 3OE1 · PDBe 3OE1 · UniProt P06672
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