Research workbench
Aathil complexed with amppcp and tmp
Analyse Aathil complexed with amppcp and tmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C9T
- Type
- protein
- Length
- 616 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
- TPS, ACP, MG
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thiamine monophosphate kinase (EC 2.7.4.16) | protein | 307 | 38% helix, 25% strand | O67883 |
| B | Thiamine monophosphate kinase (EC 2.7.4.16) | protein | 309 | 38% helix, 26% strand | O67883 |
Ligands and binding sites
- TPS · Thiamin phosphate · ligand · 2 copies · chains A, B
- ACP · Phosphomethylphosphonic acid adenylate ester · 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 | 700 | 0.80 | 0.84 | 69 | MG, TPS, ACP |
| 2 | 642 | 0.80 | 0.85 | 65 | MG, ACP, TPS |
| 3 | 90 | 0.63 | 0.90 | 21 | empty |
| 4 | 64 | 0.32 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 3169 Ų buried · 25 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 3C9T · PDBe 3C9T · UniProt O67883
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