Research workbench
Aathil complexed with amppcp
Analyse Aathil complexed with amppcp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C9S
- Type
- protein
- Length
- 606 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
- ACP, MG
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thiamine monophosphate kinase (EC 2.7.4.16) | protein | 304 | 38% helix, 27% strand | O67883 |
| B | Thiamine monophosphate kinase (EC 2.7.4.16) | protein | 302 | 39% helix, 27% strand | O67883 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 492 | 0.75 | 0.84 | 46 | ACP, MG |
| 2 | 564 | 0.74 | 0.82 | 61 | MG, ACP |
| 3 | 190 | 0.56 | 0.80 | 20 | empty |
| 4 | 76 | 0.38 | 0.78 | 11 | empty |
| 5 | 85 | 0.34 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2752 Ų buried · 15 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 3C9S · PDBe 3C9S · UniProt O67883
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