Research workbench
Aathil complexed with ADP and tpp
Analyse Aathil complexed with ADP and tpp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C9U
- Type
- protein
- Length
- 620 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiamine monophosphate kinase
- EC
- 2.7.4.16
- UniProt
- O67883
- Ligands
- TPP, ADP, MG
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thiamine monophosphate kinase (EC 2.7.4.16) | protein | 308 | 38% helix, 27% strand | O67883 |
| B | Thiamine monophosphate kinase (EC 2.7.4.16) | protein | 312 | 37% helix, 26% strand | O67883 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 535 | 0.81 | 0.87 | 63 | MG, ADP, TPP |
| 2 | 585 | 0.80 | 0.85 | 72 | MG, TPP, ADP |
| 3 | 134 | 0.64 | 0.87 | 22 | empty |
| 4 | 67 | 0.32 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 3107 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
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 O67883
- Elsewhere: RCSB PDB 3C9U · PDBe 3C9U · UniProt O67883
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