MolNFT v1 · #167920 · protein

TTLL6 bound to ATP

6VZT · Tubulin polyglutamylase TTLL6: “TTLL6 bound to ATP”. X-ray diffraction, 3 ligands (ATP, MG, SO4), 9 pockets (best druggability 0.87). MolNFT v1 #167920 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6VZT
Type: protein
Length: 806 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin polyglutamylase TTLL6; TTLL6 unregistered chain
EC: 6.-.-.-
UniProt: A4Q9E8
Ligands: ATP, MG, SO4
Pockets: 9 · best druggability 0.87

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulin polyglutamylase TTLL6 (EC 6.-.-.-)	protein	400	40% helix, 19% strand	A4Q9E8
B	Tubulin polyglutamylase TTLL6 (EC 6.-.-.-)	protein	395	39% helix, 19% strand	A4Q9E8
D	TTLL6 unregistered chain	protein	11	82% helix, 0% strand	—

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 8 copies · chains A, B
GOL · Glycerol · additive · 10 copies · chains A, B

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

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	995	0.87	0.88	101	ATP, SO4, MG, GOL
2	192	0.63	0.84	31	empty
3	244	0.63	0.82	34	empty
4	59	0.57	0.90	18	empty
5	82	0.48	0.82	24	empty

Interfaces

2 interfaces between chains.

A–B · 1064 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 181 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6VZT · TTLL6 bound to ATP · the same entry in another collection · chain A against A, TM-score 1.00
A4Q9E8 · AlphaFold monomer V2.0 prediction for tubulin polyglutamylase TTLL6 (A4Q9E8) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 A4Q9E8
Elsewhere: RCSB PDB 6VZT · PDBe 6VZT · UniProt A4Q9E8

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