Research workbench
Mtb tmk crystal structure in complex with compound 26
Analyse Mtb tmk crystal structure in complex with compound 26 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YT1
- Type
- protein
- Length
- 384 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate kinase
- EC
- 2.7.4.9
- UniProt
- P9WKE1
- Ligands
- PK5
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 191 | 51% helix, 13% strand | P9WKE1 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 193 | 50% helix, 12% strand | P9WKE1 |
Ligands and binding sites
- PK5 · 2-ethyl-~{N}-[[4-[4-[5-methyl-2,4-bis(oxidanylidene) pyrimidin-1-yl]piperidin-1-yl]phenyl]methyl]-1,2,3,5, 6,7,8,8~{A}-octahydroimidazo[1,2-a]pyridine-3-carboxamide · ligand · 2 copies · chains A, B
- CIT · Citric acid · additive · 3 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 | 154 | 0.65 | 0.86 | 24 | PK5 |
| 2 | 143 | 0.57 | 0.82 | 19 | PK5 |
| 3 | 105 | 0.39 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 849 Ų buried · 19 hydrogen bonds · protein-protein
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 P9WKE1
- Elsewhere: RCSB PDB 6YT1 · PDBe 6YT1 · UniProt P9WKE1
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