Research workbench
Crystal structure of prenyltransferase AmbP1 complexed with GSPP
Analyse Crystal structure of prenyltransferase AmbP1 complexed with GSPP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Z44
- Type
- protein
- Length
- 580 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.458
- Source
- Fischerella ambigua UTEX 1903
- Molecule
- AmbP1
- UniProt
- V5TDZ4
- Ligands
- GST, MG
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.458 · 1 distinct chain · 34% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | AmbP1 | protein | 290 | 34% helix, 31% strand | V5TDZ4 |
Ligands and binding sites
- GST · Geranyl S-thiolodiphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 928 | 0.80 | 0.82 | 87 | GST |
| 2 | 535 | 0.75 | 0.82 | 52 | GST |
| 3 | 69 | 0.36 | 0.77 | 15 | empty |
| 4 | 72 | 0.34 | 0.75 | 14 | empty |
| 5 | 69 | 0.31 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 526 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5Z44 · Crystal structure of prenyltransferase AMBP1 complexed with gspp · 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 V5TDZ4
- Elsewhere: RCSB PDB 5Z44 · PDBe 5Z44 · UniProt V5TDZ4
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