Research workbench
Crystal structure of thiamin pyrophosphokinase from S.MUTANS, northeast structural genomics consortium target SMR83
Analyse Crystal structure of thiamin pyrophosphokinase from S.MUTANS, northeast… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IHK
- Type
- protein
- Length
- 622 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiamin pyrophosphokinase
- UniProt
- Q8DVV9
- Ligands
- TPP, MG, PO4
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Thiamin pyrophosphokinase | protein | 207 | 20% helix, 34% strand | Q8DVV9 |
| B | Thiamin pyrophosphokinase | protein | 208 | 22% helix, 31% strand | Q8DVV9 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 6 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 16 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 368 | 0.72 | 0.84 | 46 | MG, PO4, TPP |
| 2 | 625 | 0.71 | 0.79 | 53 | empty |
| 3 | 381 | 0.71 | 0.83 | 46 | TPP, MG, PO4 |
| 4 | 131 | 0.48 | 0.79 | 25 | MG, PO4 |
| 5 | 119 | 0.42 | 0.76 | 28 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1676 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 138 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 121 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 3IHK · Crystal Structure of thiamin pyrophosphokinase from S.mutans, Northeast Structural… · 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
- Every structure of UniProt Q8DVV9
- Elsewhere: RCSB PDB 3IHK · PDBe 3IHK · UniProt Q8DVV9
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