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Rat protein geranylgeranyltransferase type-I complexed with L-778,123 and a sulfate anion

Analyse Rat protein geranylgeranyltransferase type-I complexed with L-778,123 and a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1S64
Type: protein
Length: 3,960 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein FARNESYLTRANSFERASE/GERANYLGERANYLTRANSFERASE type I alpha subunit…
EC: 2.5.1.58, 2.5.1.59
UniProt: Q04631, P53610
Ligands: 778, ZN, CL, SO4
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 60% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G, I, K	Protein FARNESYLTRANSFERASE/GERANYLGERANYLTRANSFERASE type I alpha subunit (EC 2.5.1.58, 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, 6% strand	P53610

Ligands and binding sites

778 · 4-[(5-{[4-(3-chlorophenyl)-3-oxopiperazin-1-yl]methyl}-1H-imidazol-1-yl)methyl]benzonitrile · ligand · 6 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
ZN · Zinc ion · metal · 6 copies · chains B, D, F, H, J, L
CL · Chloride ion · ion · 9 copies · chains C, I, D, F, G, H, J, A, K, L
SO4 · Sulfate ion · ion · 6 copies · chains B, D, F, H, J, L
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 6 copies · chains B, D, F, H, J, 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1104	0.80	0.81	94	SO4, 778, MES
2	1003	0.80	0.81	84	SO4, 778, MES
3	1075	0.78	0.80	86	SO4, 778, MES
4	1082	0.78	0.80	84	SO4, 778, MES
5	1072	0.78	0.80	79	SO4, 778, MES

Interfaces

16 interfaces between chains.

K–L · 3232 Å² buried · 55 hydrogen bonds · protein-protein
G–H · 3228 Å² buried · 54 hydrogen bonds · protein-protein
E–F · 3222 Å² buried · 52 hydrogen bonds · protein-protein
I–J · 3222 Å² buried · 56 hydrogen bonds · protein-protein
A–B · 3197 Å² buried · 53 hydrogen bonds · protein-protein

Compared structures

1S64 · Rat protein geranylgeranyltransferase type-I complexed with L-778,123 and a sulfate anion · the same entry in another collection · chain L against L, 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 1S64 · PDBe 1S64 · UniProt Q04631 · UniProt P53610

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