MolNFT v1 · #33179 · protein
Crystal structure of his-tagged S. aureus thymidylate kinase complexed with thymidine monophosphate (tmp)
2CCG: “Crystal structure of his-tagged S. aureus thymidylate kinase complexed with thymidine monophosphate (tmp)”. X-ray diffraction, 1 ligand (TMP), 2 pockets (best druggability 0.56). MolNFT v1 #33179 on GenesisL1: 3D structure, binding…
- PDB
- 2CCG
- Type
- protein
- Length
- 401 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate kinase
- EC
- 2.7.4.9
- UniProt
- P65248
- Ligands
- TMP
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 202 | 58% helix, 13% strand | P65248 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 199 | 59% helix, 14% strand | P65248 |
Ligands and binding sites
- TMP · Thymidine-5'-phosphate · ligand · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.56 | 0.76 | 43 | TMP |
| 2 | 171 | 0.47 | 0.76 | 28 | TMP |
Interfaces
1 interface between chains.
- A–B · 1021 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 2CCG · Crystal structure of His-tagged S. aureus thymidylate kinase complexed with thymidine… · the same entry in another collection · chain A against A, TM-score 1.00
- P65248 · AlphaFold monomer V2.0 prediction for thymidylate kinase (P65248) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P65248
- Elsewhere: RCSB PDB 2CCG · PDBe 2CCG · UniProt P65248
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.