MolNFT v1 · #156795 · protein
Structure of thiamine-monophosphate kinase from acinetobacter baumannii in complex with adenosine diphosphate (ADP) and thiamine diphosphate (tpp), orthorhombic crystal form
6MFM: “Structure of thiamine-monophosphate kinase from acinetobacter baumannii in complex with adenosine diphosphate…”. X-ray diffraction, 4 ligands (TPP, ADP, MG), 2 pockets (best druggability 0.79). MolNFT v1 #156795 on GenesisL1: 3D…
- PDB
- 6MFM
- Type
- protein
- Length
- 608 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
- TPP, ADP, MG, NA
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thiamine-monophosphate kinase (EC 2.7.4.16) | protein | 304 | 33% helix, 28% strand | A0A0D5YC82 |
| B | Thiamine-monophosphate kinase (EC 2.7.4.16) | protein | 304 | 33% helix, 27% strand | A0A0D5YC82 |
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 · 8 copies · chains A, B
- NA · Sodium ion · metal · 4 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 | 498 | 0.79 | 0.86 | 65 | TPP, MG, NA, ADP |
| 2 | 456 | 0.78 | 0.86 | 59 | ADP, NA, MG, TPP |
Interfaces
1 interface between chains.
- A–B · 2613 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 6MFM · 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 6MFM · PDBe 6MFM · UniProt A0A0D5YC82
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