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Thorarchaeota rab co-crystallized with GTP gamma-S

Analyse Thorarchaeota rab co-crystallized with GTP gamma-S in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7EZD
Type: protein
Length: 346 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chains: A,B
UniProt: A0A135VL07
Ligands: GDP, GSP
Pockets: 4 · best druggability 0.67

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chains: A,B	protein	171	42% helix, 26% strand	A0A135VL07
B	Chains: A,B	protein	175	36% helix, 26% strand	A0A135VL07

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · chains A
GSP · 5'-guanosine-diphosphate-monothiophosphate · ligand · chains B

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

Pockets

4 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	263	0.67	0.83	33	empty
2	240	0.50	0.74	28	empty
3	129	0.44	0.77	26	GDP
4	50	0.28	0.76	15	empty

Interfaces

1 interface between chains.

A–B · 1274 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

7EZD · Thorarchaeota Rab co-crystallized with GTP gamma-S · 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 7EZD · PDBe 7EZD · UniProt A0A135VL07

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