MolNFT v1 · #161903 · protein
Pseudomonas fluorescens pf-5 thiamine diphosphate-dependent 4- hydroxybenzoylformate decarboxylase
6QSI: “Pseudomonas fluorescens pf-5 thiamine diphosphate-dependent 4- hydroxybenzoylformate decarboxylase”. X-ray diffraction, 2 ligands (TPP, NA), 8 pockets (best druggability 0.77). MolNFT v1 #161903 on GenesisL1: 3D structure, binding…
- PDB
- 6QSI
- Type
- protein
- Length
- 1,049 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Benzoylformate decarboxylase
- EC
- 4.1.1.7
- UniProt
- Q4KB02
- Ligands
- TPP, NA
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Benzoylformate decarboxylase (EC 4.1.1.7) | protein | 525 | 39% helix, 18% strand | Q4KB02 |
| B | Benzoylformate decarboxylase (EC 4.1.1.7) | protein | 524 | 38% helix, 17% strand | Q4KB02 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 689 | 0.77 | 0.82 | 79 | TPP, NA |
| 2 | 621 | 0.77 | 0.83 | 75 | TPP, NA |
| 3 | 156 | 0.68 | 0.88 | 46 | EDO |
| 4 | 153 | 0.68 | 0.88 | 48 | EDO |
| 5 | 214 | 0.60 | 0.81 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 3616 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 6QSI · Pseudomonas fluorescens Pf-5 thiamine diphosphate-dependent 4-hydroxybenzoylformate… · the same entry in another collection · 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 Q4KB02
- Elsewhere: RCSB PDB 6QSI · PDBe 6QSI · UniProt Q4KB02
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