MolNFT v1 · #70190 · protein
Crystal structure of thymidylate kinase from ehrlichia chaffeensis at 2.15A resolution
3LD9: “Crystal structure of thymidylate kinase from ehrlichia chaffeensis at 2.15A resolution”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.74). MolNFT v1 #70190 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3LD9
- Type
- protein
- Length
- 724 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate kinase
- EC
- 2.7.4.9
- UniProt
- Q2GHN3
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 59% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 187 | 57% helix, 14% strand | Q2GHN3 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 178 | 60% helix, 15% strand | Q2GHN3 |
| C | Thymidylate kinase (EC 2.7.4.9) | protein | 175 | 59% helix, 14% strand | Q2GHN3 |
| D | Thymidylate kinase (EC 2.7.4.9) | protein | 184 | 59% helix, 14% strand | Q2GHN3 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 788 | 0.74 | 0.79 | 60 | SO4, EDO |
| 2 | 801 | 0.71 | 0.77 | 64 | SO4, EDO |
| 3 | 70 | 0.67 | 0.94 | 20 | empty |
| 4 | 177 | 0.53 | 0.79 | 25 | empty |
| 5 | 134 | 0.49 | 0.79 | 22 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1047 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1020 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 398 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 350 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 121 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3LD9 · Crystal structure of thymidylate kinase from Ehrlichia chaffeensis at 2.15A resolution · the same entry in another collection · chain D against D, TM-score 1.00
- Q2GHN3 · AlphaFold monomer V2.0 prediction for thymidylate kinase (Q2GHN3) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q2GHN3
- Elsewhere: RCSB PDB 3LD9 · PDBe 3LD9 · UniProt Q2GHN3
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