Research workbench
Crystal structure of T. acidophilum isopentenyl phosphate kinase product complex
Analyse Crystal structure of T. acidophilum isopentenyl phosphate kinase product complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LL5
- Type
- protein
- Length
- 938 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-glutamyl kinase related protein
- UniProt
- Q9HLX1
- Ligands
- ADP, IPE, ATP, IP8
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gamma-glutamyl kinase related protein | protein | 233 | 40% helix, 23% strand | Q9HLX1 |
| B | Gamma-glutamyl kinase related protein | protein | 234 | 41% helix, 23% strand | Q9HLX1 |
| C | Gamma-glutamyl kinase related protein | protein | 237 | 39% helix, 23% strand | Q9HLX1 |
| D | Gamma-glutamyl kinase related protein | protein | 234 | 41% helix, 22% strand | Q9HLX1 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- IPE · 3-methylbut-3-enyl trihydrogen diphosphate · ligand · 2 copies · chains A, B
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains C, D
- IP8 · Isopentenyl phosphate · ligand · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 489 | 0.73 | 0.82 | 68 | ADP, IPE |
| 2 | 488 | 0.68 | 0.79 | 56 | ATP, IP8 |
| 3 | 444 | 0.66 | 0.78 | 52 | ATP, IP8 |
| 4 | 261 | 0.58 | 0.78 | 42 | ADP, IPE |
| 5 | 82 | 0.53 | 0.85 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1641 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1625 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 625 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified (engineered).
Compared structures
- 3LL5 · Crystal structure of T. acidophilum isopentenyl phosphate kinase product complex · the same entry in another collection · chain D against D, TM-score 1.00
- Q9HLX1 · AlphaFold monomer V2.0 prediction for isopentenyl phosphate kinase (Q9HLX1) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9HLX1
- Elsewhere: RCSB PDB 3LL5 · PDBe 3LL5 · UniProt Q9HLX1
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