Research workbench
Structural insights into the pre-reaction state of pyruvate decarboxylase from zymomonas mobilis
Analyse Structural insights into the pre-reaction state of pyruvate decarboxylase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WVH
- Type
- protein
- Length
- 4,520 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate decarboxylase
- EC
- 4.1.1.1
- UniProt
- P06672
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate decarboxylase (EC 4.1.1.1) | protein | 566 | 39% helix, 19% strand | P06672 |
| B, E, F, V, Y, Z | Pyruvate decarboxylase (EC 4.1.1.1) | protein | 565 | 39% helix, 19% strand | P06672 |
| X | Pyruvate decarboxylase (EC 4.1.1.1) | protein | 564 | 38% helix, 19% strand | P06672 |
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 | 522 | 0.86 | 0.92 | 73 | empty |
| 2 | 995 | 0.86 | 0.87 | 146 | empty |
| 3 | 530 | 0.86 | 0.92 | 75 | empty |
| 4 | 511 | 0.86 | 0.92 | 65 | empty |
| 5 | 492 | 0.86 | 0.92 | 67 | empty |
Interfaces
15 interfaces between chains.
- V–Z · 4157 Ų buried · 77 hydrogen bonds · protein-protein
- A–B · 4149 Ų buried · 77 hydrogen bonds · protein-protein
- E–F · 4130 Ų buried · 76 hydrogen bonds · protein-protein
- X–Y · 4114 Ų buried · 75 hydrogen bonds · protein-protein
- V–Y · 1320 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 2WVH · Structural insights into the pre-reaction state of pyruvate decarboxylase from Zymomonas… · the same entry in another collection · chain Z against Z, TM-score 1.00
- P06672 · AlphaFold monomer V2.0 prediction for pyruvate decarboxylase (P06672) · a predicted model of the same protein · chain X 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 2WVH · PDBe 2WVH · UniProt P06672
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