Research workbench
TTLL6 bound to gamma-elongation analog
Analyse TTLL6 bound to gamma-elongation analog in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VZV
- Type
- protein
- Length
- 1,647 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
- S3A, ADP, S37, MG
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tubulin polyglutamylase TTLL6 (EC 6.-.-.-) | protein | 404 | 40% helix, 19% strand | A4Q9E8 |
| C | Tubulin polyglutamylase TTLL6 (EC 6.-.-.-) | protein | 405 | 39% helix, 20% strand | A4Q9E8 |
| D | Tubulin polyglutamylase TTLL6 (EC 6.-.-.-) | protein | 403 | 40% helix, 19% strand | A4Q9E8 |
| I | TTLL6 unregistered chain | protein | 15 | 87% helix, 0% strand | — |
| J | TTLL6 unregistered chain | protein | 16 | 88% helix, 0% strand | — |
Ligands and binding sites
- 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
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- S37 · (2~{S})-2-[[[(3~{S})-3-acetamido-4-oxidanyl-4-oxidanylidene-butyl]-oxidanyl-phosphoryl]methyl]pentanedioic acid · ligand · 2 copies · chains A, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 32 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 559 | 0.77 | 0.83 | 56 | GOL |
| 2 | 105 | 0.76 | 0.96 | 26 | ADP |
| 3 | 110 | 0.76 | 0.96 | 26 | ADP |
| 4 | 113 | 0.76 | 0.96 | 27 | ADP, MG |
| 5 | 105 | 0.76 | 0.96 | 27 | ADP |
Interfaces
8 interfaces between chains.
- B–D · 1157 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1150 Ų buried · 15 hydrogen bonds · protein-protein
- A–J · 278 Ų buried · 0 hydrogen bonds · protein-protein
- D–I · 242 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 237 Ų buried · 2 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 6VZV · PDBe 6VZV · UniProt A4Q9E8
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