Research workbench
Crystal structure of rab geranylgeranyltransferase from rat brain
Analyse Crystal structure of rab geranylgeranyltransferase from rat brain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DCE
- Type
- protein
- Length
- 1,792 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (rab geranylgeranyltransferase alpha subunit); Protein (rab…
- EC
- 2.5.1.-
- UniProt
- Q08602, Q08603
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Protein (rab geranylgeranyltransferase alpha subunit) (EC 2.5.1.-) | protein | 567 | 46% helix, 13% strand | Q08602 |
| B, D | Protein (rab geranylgeranyltransferase beta subunit) (EC 2.5.1.-) | protein | 329 | 52% helix, 6% strand | Q08603 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1090 | 0.85 | 0.86 | 106 | empty |
| 2 | 1003 | 0.84 | 0.85 | 90 | empty |
| 3 | 940 | 0.84 | 0.85 | 96 | empty |
| 4 | 1168 | 0.83 | 0.84 | 101 | empty |
| 5 | 532 | 0.69 | 0.79 | 36 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2979 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2913 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 592 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (formylation).
Compared structures
- 1DCE · Crystal structure of rab geranylgeranyltransferase from rat brain · the same entry in another collection · chain A against A, TM-score 1.00
- Q08603 · AlphaFold monomer V2.0 prediction for geranylgeranyl transferase type-2 subunit beta… · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q08602 · AlphaFold monomer V2.0 prediction for geranylgeranyl transferase type-2 subunit alpha… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q08602
- Every structure of UniProt Q08603
- Elsewhere: RCSB PDB 1DCE · PDBe 1DCE · UniProt Q08602 · UniProt Q08603
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