Research workbench
Protein geranylgeranyltransferase type-I complexed with geranylgeranyl diphosphate
Analyse Protein geranylgeranyltransferase type-I complexed with geranylgeranyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1N4P
- Type
- protein
- Length
- 3,968 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein FARNESYLTRANSFERASE/GERANYLGERANYLTRANSFERASE type- 1 subunit alpha…
- EC
- 2.5.1.58, 2.5.1.59
- UniProt
- Q04631, P53610
- Ligands
- GRG, GER, ZN, CL
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 59% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Protein FARNESYLTRANSFERASE/GERANYLGERANYLTRANSFERASE type- 1 subunit alpha (EC 2.5.1.58, 2.5.1.59) | protein | 314 | 68% helix, 1% strand | Q04631 |
| B, D, F, H, J, L | Geranylgeranyl transferase type-1 subunit beta (EC 2.5.1.59) | protein | 346 | 52% helix, 8% strand | P53610 |
| M, N | Fusion protein consisting of transforming protein P21B and RAS related protein rap-2B | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- GRG · Geranylgeranyl diphosphate · ligand · 6 copies · chains A, B, C, D, E, F, G, H, I, J, M, K, L, N
- GER · Geran-8-yl geran · ligand · 2 copies · chains J, M, L, N
- ZN · Zinc ion · metal · 6 copies · chains B, D, F, H, J, L
- CL · Chloride ion · ion · 9 copies · chains B, C, D, F, G, H, J, A, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 444 | 0.80 | 0.88 | 45 | GRG |
| 2 | 488 | 0.80 | 0.87 | 62 | GRG |
| 3 | 1048 | 0.78 | 0.79 | 78 | GRG |
| 4 | 975 | 0.78 | 0.79 | 66 | GRG |
| 5 | 1047 | 0.77 | 0.79 | 83 | GRG |
Interfaces
20 interfaces between chains.
- K–L · 3232 Ų buried · 53 hydrogen bonds · protein-protein
- C–D · 3223 Ų buried · 52 hydrogen bonds · protein-protein
- G–H · 3223 Ų buried · 58 hydrogen bonds · protein-protein
- I–J · 3218 Ų buried · 54 hydrogen bonds · protein-protein
- E–F · 3217 Ų buried · 55 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 lipid (geranylgeranylation).
Compared structures
- 1N4P · Protein Geranylgeranyltransferase type-I Complexed with Geranylgeranyl Diphosphate · the same entry in another collection · chain N against N, 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 Q04631
- Every structure of UniProt P53610
- Elsewhere: RCSB PDB 1N4P · PDBe 1N4P · UniProt Q04631 · UniProt P53610
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