Research workbench
Crystal structure of the tandem kinase & triphosphate tunnel metalloenzyme domain module of the TTM1 protein from arabidoposis thaliana in complex with a adenosine nucleotide analog.
Analyse Crystal structure of the tandem kinase & triphosphate tunnel metalloenzyme… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Z67
- Type
- protein
- Length
- 393 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inorganic pyrophosphatase TTM1
- EC
- 3.6.1.1
- UniProt
- Q9C9B9
- Ligands
- ACP, MG, NA
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inorganic pyrophosphatase TTM1 (EC 3.6.1.1) | protein | 393 | 32% helix, 32% strand | Q9C9B9 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains A
- MG · Magnesium ion · metal · chains A
- NA · Sodium ion · metal · chains A
- CIT · Citric acid · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 664 | 0.70 | 0.77 | 69 | CIT, ACP |
| 2 | 75 | 0.67 | 0.93 | 21 | empty |
| 3 | 139 | 0.45 | 0.76 | 20 | empty |
| 4 | 58 | 0.44 | 0.83 | 18 | empty |
| 5 | 68 | 0.33 | 0.76 | 16 | empty |
Modifications
Observed in the structure: 7 modified (engineered).
Compared structures
- 7Z67 · Crystal structure of the tandem kinase & triphosphate tunnel metalloenzyme domain module… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9C9B9 · AlphaFold monomer V2.0 prediction for inorganic pyrophosphatase TTM1 (Q9C9B9) · a predicted model of the same protein · chain A against A, TM-score 0.54
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 Q9C9B9
- Elsewhere: RCSB PDB 7Z67 · PDBe 7Z67 · UniProt Q9C9B9
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