Research workbench
Crystal structure of ATTTM3 in complex with tripolyphosphate and magnesium ion (form a)
Analyse Crystal structure of ATTTM3 in complex with tripolyphosphate and magnesium ion… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A5Y
- Type
- protein
- Length
- 422 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Triphosphate tunel metalloenzyme 3
- EC
- 3.6.1.3, 3.6.1.25
- UniProt
- Q9SIY3
- Ligands
- 3PO, MG
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Triphosphate tunel metalloenzyme 3 (EC 3.6.1.3, 3.6.1.25) | protein | 211 | 31% helix, 44% strand | Q9SIY3 |
Ligands and binding sites
- 3PO · Triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 558 | 0.75 | 0.82 | 66 | EDO |
| 2 | 321 | 0.68 | 0.82 | 42 | MG, 3PO |
| 3 | 278 | 0.66 | 0.82 | 41 | MG, 3PO |
Interfaces
1 interface between chains.
- A–B · 716 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5A5Y · Crystal structure of AtTTM3 in complex with tripolyphosphate and magnesium ion (form A) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9SIY3 · AlphaFold monomer V2.0 prediction for triphosphate tunnel metalloenzyme 3 (Q9SIY3) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q9SIY3
- Elsewhere: RCSB PDB 5A5Y · PDBe 5A5Y · UniProt Q9SIY3
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