Research workbench
X-ray crystallographic structure of inorganic pyrophosphatase at 298K from archaeon thermococcus thioreducens
Analyse X-ray crystallographic structure of inorganic pyrophosphatase at 298K from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I98
- Type
- protein
- Length
- 1,049 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Th-ipp
- Ligands
- ACE, CA
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F | Th-ipp | protein | 175 | 25% helix, 33% strand | — |
| E | Th-ipp | protein | 174 | 25% helix, 33% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains E
- CA · Calcium ion · metal · 6 copies · chains A, B, C, D, E, F
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains A, F
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 355 | 0.81 | 0.90 | 33 | empty |
| 2 | 367 | 0.78 | 0.88 | 31 | empty |
| 3 | 181 | 0.59 | 0.82 | 31 | empty |
| 4 | 163 | 0.56 | 0.81 | 26 | empty |
| 5 | 249 | 0.56 | 0.78 | 29 | CA |
Interfaces
6 interfaces between chains.
- A–C · 855 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 843 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 834 Ų buried · 8 hydrogen bonds · protein-protein
- C–E · 820 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 800 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3I98 · X-ray crystallographic structure of Inorganic Pyrophosphatase at 298K from archaeon… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 3I98 · PDBe 3I98
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