Research workbench
The crystal structure of acyltransferase in complex with decanoyl-CoA and tei pseudoaglycone
Analyse The crystal structure of acyltransferase in complex with decanoyl-CoA and tei… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MFP
- Type
- protein
- Length
- 330 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein TCP24; Teicoplanin pseudoaglycone
- EC
- 2.3.1.-
- UniProt
- Q70AY4
- Ligands
- COA, DKA, NAG, MAN, GCS, SO4
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uncharacterized protein TCP24 (EC 2.3.1.-) | protein | 323 | 52% helix, 10% strand | Q70AY4 |
| B | Teicoplanin pseudoaglycone | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- COA · Coenzyme A · ligand · chains A, B
- DKA · Decanoic acid · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A, B
- MAN · alpha-D-mannopyranose · sugar · chains B
- GCS · 2-amino-2-deoxy-beta-D-glucopyranose · sugar · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 763 | 0.77 | 0.81 | 79 | COA, NAG, GCS, DKA |
| 2 | 147 | 0.39 | 0.73 | 23 | empty |
| 3 | 60 | 0.30 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 519 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 modified, 3 glycan (nonstandard, glycosylation).
Compared structures
- 4MFP · The crystal structure of acyltransferase in complex with decanoyl-CoA and Tei… · 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 Q70AY4
- Elsewhere: RCSB PDB 4MFP · PDBe 4MFP · UniProt Q70AY4
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