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
- 4Q1K
- Type
- protein
- Length
- 729 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
- Ligands
- PO4
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 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 | 236 | 50% helix, 19% strand | P40802 |
| B | Polyketide biosynthesis enoyl-CoA isomerase pksi (EC 4.-.-.-) | protein | 247 | 51% helix, 19% strand | P40802 |
| C | Polyketide biosynthesis enoyl-CoA isomerase pksi (EC 4.-.-.-) | protein | 246 | 50% helix, 18% strand | P40802 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.77 | 0.79 | 70 | GOL, PO4 |
| 2 | 256 | 0.71 | 0.86 | 41 | empty |
| 3 | 364 | 0.70 | 0.82 | 55 | empty |
| 4 | 262 | 0.64 | 0.81 | 41 | empty |
| 5 | 322 | 0.55 | 0.75 | 49 | GOL |
Interfaces
3 interfaces between chains.
- B–C · 1118 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1094 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1043 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4Q1K · 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 C 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 4Q1K · PDBe 4Q1K · UniProt P40802
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