Research workbench
Crystal structure of the benzoylformate decarboxylase variant L461A from pseudomonas putida
Analyse Crystal structure of the benzoylformate decarboxylase variant L461A from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V3W
- Type
- protein
- Length
- 2,104 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Benzoylformate decarboxylase
- EC
- 4.1.1.7
- UniProt
- P20906
- Ligands
- TPP, MG, SO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Benzoylformate decarboxylase (EC 4.1.1.7) | protein | 526 | 40% helix, 19% strand | P20906 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 4 copies · chains A, C, B, D
- MG · Magnesium ion · metal · 6 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, B, 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 593 | 0.88 | 0.93 | 94 | empty |
| 2 | 370 | 0.83 | 0.92 | 57 | empty |
| 3 | 210 | 0.81 | 0.95 | 38 | empty |
| 4 | 530 | 0.78 | 0.85 | 77 | SO4, TPP |
| 5 | 507 | 0.78 | 0.85 | 62 | MG, TPP, SO4 |
Interfaces
6 interfaces between chains.
- B–D · 3625 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 3618 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1716 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 1694 Ų buried · 34 hydrogen bonds · protein-protein
- A–D · 558 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2V3W · Crystal structure of the benzoylformate decarboxylase variant L461A from Pseudomonas… · the same entry in another collection · chain A against A, TM-score 1.00
- P20906 · AlphaFold monomer V2.0 prediction for benzoylformate decarboxylase (P20906) · 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 P20906
- Elsewhere: RCSB PDB 2V3W · PDBe 2V3W · UniProt P20906
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