Research workbench
Protein geranylgeranyltransferase type-I complexed with a ggpp analog and a kkksktkcvil peptide
Analyse Protein geranylgeranyltransferase type-I complexed with a ggpp analog and a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1N4Q
- Type
- protein
- Length
- 3,990 residues
- Chains
- 18
- 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
- MGM, GER, ZN, CL
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 60% helix, 4% 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 | 69% 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, 6% strand | P53610 |
| M, N, O, P, Q, R | Fusion protein consisting of transforming protein P21B and RAS related protein rap-2B | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- MGM · 2-[methyl-(5-geranyl-4-methyl-pent-3-enyl)-amino]-ethyl-diphosphate · ligand · 6 copies · chains A, B, M, C, D, N, E, F, O, G, H, P, I, J, Q, K, L, R
- GER · Geran-8-yl geran · ligand · chains L, R
- ZN · Zinc ion · metal · 6 copies · chains B, M, D, N, F, O, H, P, J, Q, L
- CL · Chloride ion · ion · 7 copies · chains C, I, D, F, G, H, J, A, K
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 | 718 | 0.84 | 0.87 | 87 | MGM |
| 2 | 880 | 0.83 | 0.85 | 97 | MGM |
| 3 | 401 | 0.81 | 0.89 | 46 | MGM |
| 4 | 384 | 0.81 | 0.89 | 44 | MGM |
| 5 | 435 | 0.80 | 0.87 | 44 | MGM |
Interfaces
28 interfaces between chains.
- K–L · 3257 Ų buried · 54 hydrogen bonds · protein-protein
- I–J · 3225 Ų buried · 57 hydrogen bonds · protein-protein
- C–D · 3196 Ų buried · 53 hydrogen bonds · protein-protein
- G–H · 3167 Ų buried · 53 hydrogen bonds · protein-protein
- E–F · 3159 Ų buried · 49 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 lipid (geranylgeranylation).
Compared structures
- 1N4Q · Protein Geranylgeranyltransferase type-I Complexed with a GGPP Analog and a KKKSKTKCVIL… · the same entry in another collection · chain K against K, 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 1N4Q · PDBe 1N4Q · UniProt Q04631 · UniProt P53610
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