Research workbench
Rat protein geranylgeranyltransferase type-I complexed with a ggpp analog and a frekkffcail peptide derived from the heterotrimeric G protein gamma-2 subunit
Analyse Rat 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
- 1TNY
- Type
- protein
- Length
- 3,990 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Geranylgeranyltransferase type I alpha subunit; Geranylgeranyl transferase type I beta…
- EC
- 2.5.1.59
- UniProt
- Q04631, P53610
- Ligands
- MGM, ZN, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 59% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Geranylgeranyltransferase type I alpha subunit (EC 2.5.1.59) | protein | 314 | 67% helix, 1% strand | Q04631 |
| B, D, F, H, J, L | Geranylgeranyl transferase type I beta subunit (EC 2.5.1.59) | protein | 346 | 53% helix, 8% strand | P53610 |
| M, N, O, P, Q, R | Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-2 subunit | 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
- ZN · Zinc ion · metal · 6 copies · chains B, M, D, N, F, O, H, P, J, Q, L, R
- CL · Chloride ion · ion · 6 copies · chains B, D, F, H, J, L
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains F
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 | 506 | 0.81 | 0.88 | 65 | MGM |
| 2 | 595 | 0.81 | 0.86 | 83 | MGM |
| 3 | 895 | 0.81 | 0.83 | 94 | MGM |
| 4 | 532 | 0.81 | 0.87 | 68 | MGM |
| 5 | 735 | 0.81 | 0.84 | 70 | MGM |
Interfaces
28 interfaces between chains.
- K–L · 3257 Ų buried · 56 hydrogen bonds · protein-protein
- C–D · 3226 Ų buried · 54 hydrogen bonds · protein-protein
- I–J · 3224 Ų buried · 58 hydrogen bonds · protein-protein
- G–H · 3187 Ų buried · 55 hydrogen bonds · protein-protein
- E–F · 3182 Ų buried · 57 hydrogen bonds · protein-protein
Compared structures
- 1TNY · Rat Protein Geranylgeranyltransferase Type-I Complexed with a GGPP analog and a… · 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 1TNY · PDBe 1TNY · UniProt Q04631 · UniProt P53610
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