MolNFT v1 · #115517 · protein
Structure of thiamine-monophosphate kinase from acinetobacter baumannii in complex with adenosine diphosphate (ADP) and thiamine diphosphate (tpp)
5CM7: “Structure of thiamine-monophosphate kinase from acinetobacter baumannii in complex with adenosine diphosphate…”. X-ray diffraction, 5 ligands (ADP, TPP, CA), 3 pockets (best druggability 0.77). MolNFT v1 #115517 on GenesisL1: 3D…
- PDB
- 5CM7
- Type
- protein
- Length
- 609 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
- ADP, TPP, CA, MG, NA
- Pockets
- 3 · best druggability 0.77
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 | 305 | 32% helix, 27% strand | A0A0D5YC82 |
| B | Thiamine-monophosphate kinase (EC 2.7.4.16) | protein | 304 | 33% helix, 27% strand | A0A0D5YC82 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 6 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 496 | 0.77 | 0.85 | 60 | ADP, CA, MG, TPP, NA |
| 2 | 506 | 0.77 | 0.85 | 59 | NA, TPP, CA, MG, ADP |
| 3 | 55 | 0.35 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2661 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 5CM7 · 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 5CM7 · PDBe 5CM7 · UniProt A0A0D5YC82
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