Research workbench
Structure and mechanism of a dehydratase/decarboxylase enzyme couple involved in polyketide beta-branching
Analyse Structure and mechanism of a dehydratase/decarboxylase enzyme couple involved… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q1H
- Type
- protein
- Length
- 733 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.93
- Source
- Bacillus subtilis
- Molecule
- Polyketide biosynthesis enoyl-CoA isomerase PksI
- EC
- 4.-.-.-
- UniProt
- P40802
- Ligands
- NA
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · resolution 1.93 · 3 distinct chains · 50% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyketide biosynthesis enoyl-CoA isomerase PksI (EC 4.-.-.-) | protein | 253 | 50% helix, 19% strand | P40802 |
| B | Polyketide biosynthesis enoyl-CoA isomerase PksI (EC 4.-.-.-) | protein | 246 | 52% helix, 18% strand | P40802 |
| C | Polyketide biosynthesis enoyl-CoA isomerase PksI (EC 4.-.-.-) | protein | 234 | 48% helix, 20% strand | P40802 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- GOL · Glycerol · additive · 8 copies · chains A, C, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 996 | 0.77 | 0.79 | 70 | GOL |
| 2 | 286 | 0.72 | 0.85 | 44 | GOL |
| 3 | 245 | 0.65 | 0.82 | 38 | empty |
| 4 | 94 | 0.64 | 0.90 | 23 | empty |
| 5 | 167 | 0.53 | 0.79 | 35 | GOL |
Interfaces
3 interfaces between chains.
- B–C · 1140 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1129 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1058 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4Q1H · Structure and mechanism of a DEHYDRATASE/DECARBOXYLASE enzyme couple involved in… · the same entry in another collection · chain A against A, TM-score 1.00
- P40802 · AlphaFold monomer V2.0 prediction for putative polyketide biosynthesis enoyl-CoA… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P40802
- Elsewhere: RCSB PDB 4Q1H · PDBe 4Q1H · UniProt P40802
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