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Rat protein geranylgeranyltransferase type-I complexed with a ggpp analog and a gcincckvl peptide derived from rhob

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: 1TNU
Type: protein
Length: 3,996 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 0.84

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	Geranylgeranyltransferase type I alpha subunit (EC 2.5.1.59)	protein	314	69% 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, 7% strand	P53610
M, N, O, P, Q, R	Transforming protein rhob	protein	6	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 · 3 copies · chains D, F, H
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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	957	0.84	0.85	102	MGM
2	728	0.83	0.86	79	MGM
3	436	0.81	0.89	46	MGM
4	412	0.81	0.89	47	MGM
5	416	0.81	0.89	46	MGM

Interfaces

28 interfaces between chains.

K–L · 3278 Å² buried · 54 hydrogen bonds · protein-protein
C–D · 3230 Å² buried · 54 hydrogen bonds · protein-protein
I–J · 3219 Å² buried · 53 hydrogen bonds · protein-protein
G–H · 3213 Å² buried · 56 hydrogen bonds · protein-protein
E–F · 3206 Å² buried · 51 hydrogen bonds · protein-protein

Compared structures

1TNU · Rat Protein Geranylgeranyltransferase Type-I Complexed with a GGPP analog and a GCINCCKVL… · 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 1TNU · PDBe 1TNU · UniProt Q04631 · UniProt P53610

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