MolNFT v1 · #112564 · protein
Crystal structure of zymomonas mobilis pyruvate decarboxylase variant GLU473ALA
4ZP1: “Crystal structure of zymomonas mobilis pyruvate decarboxylase variant GLU473ALA”. X-ray diffraction, 3 ligands (TPP, MG, NI), 20 pockets (best druggability 0.86). MolNFT v1 #112564 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4ZP1
- Type
- protein
- Length
- 2,260 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
- TPP, MG, NI
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pyruvate decarboxylase (EC 4.1.1.1) | protein | 565 | 40% helix, 19% strand | P06672 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- NI · Nickel (II) ion · metal · 2 copies · chains A, C, B, D
- GOL · Glycerol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1199 | 0.86 | 0.87 | 145 | NI |
| 2 | 202 | 0.83 | 0.97 | 43 | MG, TPP |
| 3 | 205 | 0.83 | 0.96 | 42 | TPP |
| 4 | 211 | 0.83 | 0.96 | 45 | MG, TPP |
| 5 | 191 | 0.83 | 0.97 | 42 | TPP |
Interfaces
6 interfaces between chains.
- A–B · 4266 Ų buried · 77 hydrogen bonds · protein-protein
- C–D · 4217 Ų buried · 76 hydrogen bonds · protein-protein
- B–C · 1323 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 1283 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 666 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4ZP1 · Crystal structure of Zymomonas mobilis pyruvate decarboxylase variant Glu473Ala · 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 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 P06672
- Elsewhere: RCSB PDB 4ZP1 · PDBe 4ZP1 · UniProt P06672
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