MolNFT v1 · #167918 · protein
Engineered TTLL6 bound to the initiation analog
6VZR · Tubulin polyglutamylase TTLL6: “Engineered TTLL6 bound to the initiation analog”. X-ray diffraction, 3 ligands (2TI, ADP, MG), 20 pockets (best druggability 0.82). MolNFT v1 #167918 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6VZR
- Type
- protein
- Length
- 1,633 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin polyglutamylase TTLL6; TTLL6 unregistered chain
- EC
- 6.-.-.-
- UniProt
- A4Q9E8
- Ligands
- 2TI, ADP, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin polyglutamylase TTLL6 (EC 6.-.-.-) | protein | 400 | 39% helix, 21% strand | A4Q9E8 |
| B | Tubulin polyglutamylase TTLL6 (EC 6.-.-.-) | protein | 402 | 39% helix, 21% strand | A4Q9E8 |
| C, D | Tubulin polyglutamylase TTLL6 (EC 6.-.-.-) | protein | 404 | 40% helix, 21% strand | A4Q9E8 |
| F | TTLL6 unregistered chain | protein | 12 | 75% helix, 0% strand | — |
| G | TTLL6 unregistered chain | protein | 11 | 73% helix, 0% strand | — |
Ligands and binding sites
- 2TI · (2~{S})-2-[[[(3~{R})-3-acetamido-4-(ethylamino)-4-oxidanylidene-butyl]-phosphonooxy-phosphoryl]methyl]pentanedioic acid · ligand · 4 copies · chains A, C, B, D
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 26 copies · chains A, B, C, 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 | 882 | 0.82 | 0.84 | 106 | 2TI |
| 2 | 591 | 0.77 | 0.83 | 55 | empty |
| 3 | 109 | 0.76 | 0.96 | 27 | ADP, MG |
| 4 | 109 | 0.76 | 0.96 | 24 | ADP, MG |
| 5 | 104 | 0.75 | 0.96 | 25 | ADP, MG |
Interfaces
8 interfaces between chains.
- A–C · 1134 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 1080 Ų buried · 8 hydrogen bonds · protein-protein
- B–G · 194 Ų buried · 0 hydrogen bonds · protein-protein
- C–F · 178 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 167 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 6VZR · PDBe 6VZR · UniProt A4Q9E8
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