MolNFT v1 · #56406 · protein
Crystal structure of adenosine phosphate-isopentenyltransferase complexed with diphosphate
2ZE8 · Isopentenyl transferase: “Crystal structure of adenosine phosphate-isopentenyltransferase complexed with diphosphate”. X-ray diffraction, 1 ligand (POP), 6 pockets (best druggability 0.83). MolNFT v1 #56406 on GenesisL1: 3D…
- PDB
- 2ZE8
- Type
- protein
- Length
- 904 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isopentenyl transferase
- EC
- 2.5.1.27
- UniProt
- P58758
- Ligands
- POP
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Isopentenyl transferase (EC 2.5.1.27) | protein | 226 | 53% helix, 11% strand | P58758 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.83 | 0.84 | 86 | empty |
| 2 | 1181 | 0.83 | 0.84 | 94 | empty |
| 3 | 347 | 0.73 | 0.85 | 44 | POP |
| 4 | 355 | 0.72 | 0.84 | 44 | POP |
| 5 | 349 | 0.72 | 0.84 | 45 | POP |
Interfaces
2 interfaces between chains.
- A–C · 830 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 817 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2ZE8 · Crystal Structure of adenosine phosphate-isopentenyltransferase complexed with diphosphate · the same entry in another collection · chain A against A, TM-score 1.00
- P58758 · AlphaFold monomer V2.0 prediction for adenylate dimethylallyltransferase (P58758) · a predicted model of the same protein · chain A 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 P58758
- Elsewhere: RCSB PDB 2ZE8 · PDBe 2ZE8 · UniProt P58758
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