Research workbench
Crystal structure of prenyltransferase AMBP1 PH6.5 complexed with gspp and cis-indolyl vinyl isonitrile
Analyse Crystal structure of prenyltransferase AMBP1 PH6.5 complexed with gspp and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Z45
- Type
- protein
- Length
- 576 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AMBP1
- UniProt
- V5TDZ4
- Ligands
- GST, 8XL, MG
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | AMBP1 | protein | 289 | 38% helix, 31% strand | V5TDZ4 |
| B | AMBP1 | protein | 287 | 36% helix, 31% strand | V5TDZ4 |
Ligands and binding sites
- GST · Geranyl S-thiolodiphosphate · ligand · 2 copies · chains A, B
- 8XL · 3-[(Z)-2-isocyanoethenyl]-1H-indole · ligand · chains 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
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 952 | 0.80 | 0.82 | 97 | GST, 8XL |
| 2 | 346 | 0.68 | 0.82 | 31 | GST |
| 3 | 175 | 0.55 | 0.80 | 32 | empty |
| 4 | 82 | 0.35 | 0.75 | 18 | empty |
| 5 | 71 | 0.33 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 513 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5Z45 · Crystal structure of prenyltransferase AmbP1 pH6.5 complexed with GSPP and cis-indolyl… · 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 5Z45 · PDBe 5Z45 · UniProt V5TDZ4
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