MolNFT v1 · #76384 · protein
Crystal structure of the mycobacterium tuberculosis thymidylate synthase (thya) bound to dump
3QJ7: “Crystal structure of the mycobacterium tuberculosis thymidylate synthase (thya) bound to dump”. X-ray diffraction, 2 ligands (UMP, SPM), 15 pockets (best druggability 0.73). MolNFT v1 #76384 on GenesisL1: 3D structure, binding sites…
- PDB
- 3QJ7
- Type
- protein
- Length
- 1,037 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P67044
- Ligands
- UMP, SPM
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase (EC 2.1.1.45) | protein | 260 | 37% helix, 26% strand | P67044 |
| B | Thymidylate synthase (EC 2.1.1.45) | protein | 257 | 35% helix, 26% strand | P67044 |
| C | Thymidylate synthase (EC 2.1.1.45) | protein | 259 | 36% helix, 25% strand | P67044 |
| D | Thymidylate synthase (EC 2.1.1.45) | protein | 261 | 35% helix, 26% strand | P67044 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 4 copies · chains A, C, B, D
- SPM · Spermine · ligand · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.73 | 0.89 | 38 | SPM |
| 2 | 455 | 0.68 | 0.79 | 35 | UMP |
| 3 | 483 | 0.65 | 0.77 | 41 | UMP |
| 4 | 369 | 0.62 | 0.77 | 30 | UMP |
| 5 | 378 | 0.62 | 0.77 | 34 | UMP |
Interfaces
3 interfaces between chains.
- A–C · 2150 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 2057 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 794 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3QJ7 · Crystal Structure of the Mycobacterium tuberculosis Thymidylate synthase (ThyA) bound to… · 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 P67044
- Elsewhere: RCSB PDB 3QJ7 · PDBe 3QJ7 · UniProt P67044
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