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Thorarchaeota rab bound to GDP

Analyse Thorarchaeota rab bound to GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7EZB
Type: protein
Length: 345 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thorarchaeota rab
UniProt: A0A135VL07
Ligands: GDP, MG
Pockets: 6 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thorarchaeota rab	protein	174	40% helix, 27% strand	A0A135VL07
B	Thorarchaeota rab	protein	171	34% helix, 26% strand	A0A135VL07

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

6 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	249	0.70	0.85	37	empty
2	129	0.44	0.77	26	GDP, MG
3	111	0.43	0.78	17	empty
4	144	0.40	0.73	17	empty
5	79	0.32	0.74	23	GDP, MG

Interfaces

1 interface between chains.

A–B · 1297 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

7EZB · Thorarchaeota Rab bound to GDP · 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 7EZB · PDBe 7EZB · UniProt A0A135VL07

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