MolNFT v1 · #177939 · protein

Thorarchaeota rab GTP-gamma-S/MG2+ (soak)

7EZE: “Thorarchaeota rab GTP-gamma-S/MG2+ (soak)”. X-ray diffraction, 2 ligands (GSP, MG), 3 pockets (best druggability 0.67). MolNFT v1 #177939 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7EZE
Type: protein
Length: 342 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thorarchaeota rab
UniProt: A0A135VL07
Ligands: GSP, MG
Pockets: 3 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thorarchaeota rab	protein	170	42% helix, 25% strand	A0A135VL07
B	Thorarchaeota rab	protein	172	37% helix, 26% strand	A0A135VL07

Ligands and binding sites

GSP · 5'-guanosine-diphosphate-monothiophosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	290	0.67	0.82	33	empty
2	177	0.46	0.75	20	empty
3	65	0.34	0.76	20	GSP

Interfaces

1 interface between chains.

A–B · 1321 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

7EZE · Thorarchaeota Rab GTP-gamma-S/Mg2+ (soak) · the same entry in another collection · chain A against A, 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 A0A135VL07
Elsewhere: RCSB PDB 7EZE · PDBe 7EZE · UniProt A0A135VL07

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