Research workbench
Structure of thiamine-monophosphate kinase from acinetobacter baumannii in complex with amppnp and thiamine-monophosphate
Analyse Structure of thiamine-monophosphate kinase from acinetobacter baumannii in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DD7
- Type
- protein
- Length
- 610 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
- A0A0D5YC82
- Ligands
- ANP, TPS, MG, K
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thiamine-monophosphate kinase (EC 2.7.4.16) | protein | 305 | 33% helix, 27% strand | A0A0D5YC82 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- TPS · Thiamin phosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 8 copies · chains A, B
- K · Potassium ion · metal · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 469 | 0.79 | 0.86 | 63 | MG, K, TPS, ANP |
| 2 | 461 | 0.79 | 0.86 | 61 | ANP, MG, K, TPS |
Interfaces
1 interface between chains.
- A–B · 2691 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 5DD7 · Structure of thiamine-monophosphate kinase from Acinetobacter baumannii in complex with… · 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 A0A0D5YC82
- Elsewhere: RCSB PDB 5DD7 · PDBe 5DD7 · UniProt A0A0D5YC82
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