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
- 4Q1I
- Type
- protein
- Length
- 673 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyketide biosynthesis enoyl-CoA isomerase pksi
- EC
- 4.-.-.-
- UniProt
- P40802
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyketide biosynthesis enoyl-CoA isomerase pksi (EC 4.-.-.-) | protein | 215 | 45% helix, 23% strand | P40802 |
| B | Polyketide biosynthesis enoyl-CoA isomerase pksi (EC 4.-.-.-) | protein | 246 | 51% helix, 18% strand | P40802 |
| C | Polyketide biosynthesis enoyl-CoA isomerase pksi (EC 4.-.-.-) | protein | 212 | 45% helix, 23% strand | P40802 |
Ligands and binding sites
- GOL · Glycerol · additive · 6 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 933 | 0.77 | 0.79 | 90 | GOL |
| 2 | 353 | 0.72 | 0.84 | 47 | GOL |
| 3 | 113 | 0.43 | 0.77 | 21 | empty |
| 4 | 56 | 0.33 | 0.78 | 14 | empty |
| 5 | 58 | 0.26 | 0.73 | 13 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1126 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 957 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 873 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4Q1I · 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 4Q1I · PDBe 4Q1I · UniProt P40802
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