MolNFT v1 · #135018 · protein
Zymomonas mobilis pyruvate decarboxylase mutant pdc-2.3
5TMA: “Zymomonas mobilis pyruvate decarboxylase mutant pdc-2.3”. X-ray diffraction, 3 ligands (TPP, MG, SO4), 12 pockets (best druggability 0.76). MolNFT v1 #135018 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5TMA
- Type
- protein
- Length
- 1,128 residues
- Chains
- 2
- 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, SO4
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate decarboxylase (EC 4.1.1.1) | protein | 567 | 40% helix, 18% strand | P06672 |
| B | Pyruvate decarboxylase (EC 4.1.1.1) | protein | 561 | 40% helix, 19% strand | P06672 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 16 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 721 | 0.76 | 0.81 | 70 | SO4, EDO |
| 2 | 134 | 0.67 | 0.89 | 34 | empty |
| 3 | 183 | 0.64 | 0.85 | 43 | empty |
| 4 | 124 | 0.61 | 0.86 | 33 | TPP |
| 5 | 109 | 0.60 | 0.86 | 33 | TPP, MG |
Interfaces
1 interface between chains.
- A–B · 1243 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
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 P06672
- Elsewhere: RCSB PDB 5TMA · PDBe 5TMA · UniProt P06672
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