MolNFT v1 · #13975 · protein
Structure of rab escort protein-1 in complex with rab geranylgeranyl transferase and isoprenoid
1LTX · Rab geranylgeranyltransferase alpha subunit: “Structure of rab escort protein-1 in complex with rab geranylgeranyl transferase and isoprenoid”. X-ray diffraction, 3 ligands (FAR, ZN, CL), 18 pockets (best druggability 0.83). MolNFT…
- PDB
- 1LTX
- Type
- protein
- Length
- 1,352 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rab geranylgeranyltransferase alpha subunit; Rab geranylgeranyltransferase beta subunit…
- EC
- 2.5.1.-
- UniProt
- Q08602, Q08603, P37727
- Ligands
- FAR, ZN, CL
- Pockets
- 18 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rab geranylgeranyltransferase alpha subunit (EC 2.5.1.-) | protein | 536 | 47% helix, 13% strand | Q08602 |
| B | Rab geranylgeranyltransferase beta subunit (EC 2.5.1.-) | protein | 318 | 49% helix, 6% strand | Q08603 |
| R | Rab escort protein 1 | protein | 494 | 32% helix, 25% strand | P37727 |
| P | Aaaa | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- FAR · Farnesyl · ligand · chains A, B, P
- ZN · Zinc ion · metal · chains B
- CL · Chloride ion · ion · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 662 | 0.83 | 0.87 | 65 | ZN, FAR |
| 2 | 922 | 0.83 | 0.84 | 94 | empty |
| 3 | 437 | 0.64 | 0.77 | 57 | empty |
| 4 | 424 | 0.63 | 0.77 | 48 | empty |
| 5 | 178 | 0.55 | 0.79 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2345 Ų buried · 33 hydrogen bonds · protein-protein
- A–R · 677 Ų buried · 8 hydrogen bonds · protein-protein
- B–P · 199 Ų buried · 2 hydrogen bonds · protein-protein
- A–P · 88 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1LTX · Structure of Rab Escort Protein-1 in complex with Rab geranylgeranyl transferase and… · 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 0.99
- 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 0.98
- P37727 · AlphaFold monomer V2.0 prediction for rab proteins geranylgeranyltransferase component a… · a predicted model of the same protein · chain R against A, TM-score 0.97
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
- Every structure of UniProt P37727
- Elsewhere: RCSB PDB 1LTX · PDBe 1LTX · UniProt Q08602 · UniProt Q08603 · UniProt P37727
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