MolNFT v1 · #167919 · protein
Engineered TTLL6 mutant bound to gamma-elongation analog
6VZS · Tubulin polyglutamylase TTLL6: “Engineered TTLL6 mutant bound to gamma-elongation analog”. X-ray diffraction, 3 ligands (ADP, S3A, MG), 20 pockets (best druggability 0.83). MolNFT v1 #167919 on GenesisL1: 3D structure, binding sites…
- PDB
- 6VZS
- Type
- protein
- Length
- 1,613 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin polyglutamylase TTLL6
- EC
- 6.-.-.-
- UniProt
- A4Q9E8
- Ligands
- ADP, S3A, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Tubulin polyglutamylase TTLL6 (EC 6.-.-.-) | protein | 404 | 39% helix, 19% strand | A4Q9E8 |
| B | Tubulin polyglutamylase TTLL6 (EC 6.-.-.-) | protein | 401 | 39% helix, 20% strand | A4Q9E8 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- S3A · (2~{S})-2-[[[(3~{R})-3-acetamido-4-oxidanyl-4-oxidanylidene-butyl]-phosphonooxy-phosphoryl]methyl]pentanedioic acid · ligand · 4 copies · chains A, C, B, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 33 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 695 | 0.83 | 0.87 | 85 | ADP, S3A, MG |
| 2 | 437 | 0.81 | 0.89 | 60 | ADP, S3A, GOL, MG |
| 3 | 420 | 0.81 | 0.89 | 61 | ADP, S3A, MG |
| 4 | 112 | 0.75 | 0.95 | 27 | ADP, MG |
| 5 | 337 | 0.75 | 0.87 | 53 | S3A |
Interfaces
4 interfaces between chains.
- A–C · 1210 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1178 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 236 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 222 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 6VZS · PDBe 6VZS · UniProt A4Q9E8
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