Research workbench
Crystal structure of thymidylate kinase from staphylococcus aureus in complex with thymidine monophosphate
Analyse Crystal structure of thymidylate kinase from staphylococcus aureus in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DWJ
- Type
- protein
- Length
- 1,589 residues
- Chains
- 8
- 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
- 16 · best druggability 0.71
Structure
x-ray diffraction · 6 distinct chains · 59% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Thymidylate kinase (EC 2.7.4.9) | protein | 200 | 59% helix, 14% strand | P65248 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 203 | 59% helix, 13% strand | P65248 |
| C | Thymidylate kinase (EC 2.7.4.9) | protein | 202 | 58% helix, 13% strand | P65248 |
| E, F | Thymidylate kinase (EC 2.7.4.9) | protein | 201 | 59% helix, 13% strand | P65248 |
| G | Thymidylate kinase (EC 2.7.4.9) | protein | 190 | 60% helix, 14% strand | P65248 |
| H | Thymidylate kinase (EC 2.7.4.9) | protein | 192 | 60% helix, 14% strand | P65248 |
Ligands and binding sites
- TMP · Thymidine-5'-phosphate · ligand · 7 copies · chains A, B, C, D, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.71 | 0.75 | 88 | empty |
| 2 | 1002 | 0.71 | 0.75 | 85 | TMP |
| 3 | 239 | 0.51 | 0.76 | 38 | TMP |
| 4 | 204 | 0.50 | 0.76 | 31 | TMP |
| 5 | 145 | 0.49 | 0.78 | 25 | TMP |
Interfaces
10 interfaces between chains.
- E–G · 1050 Ų buried · 12 hydrogen bonds · protein-protein
- F–H · 1042 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1032 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1026 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 415 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4DWJ · Crystal structure of Thymidylate Kinase from Staphylococcus aureus in complex with… · the same entry in another collection · chain H against H, TM-score 1.00
- P65248 · AlphaFold monomer V2.0 prediction for thymidylate kinase (P65248) · a predicted model of the same protein · chain G against A, TM-score 0.94
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 4DWJ · PDBe 4DWJ · UniProt P65248
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