MolNFT v1 · #6093 · protein
Crystal structure of thymidylate synthase from pneumocystis carinii bound to dump and BW1843U89
1F28: “Crystal structure of thymidylate synthase from pneumocystis carinii bound to dump and BW1843U89”. X-ray diffraction, 2 ligands (UMP, F89), 15 pockets (best druggability 0.80). MolNFT v1 #6093 on GenesisL1: 3D structure, binding…
- PDB
- 1F28
- Type
- protein
- Length
- 1,180 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P13100
- Ligands
- UMP, F89
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Thymidylate synthase (EC 2.1.1.45) | protein | 295 | 35% helix, 22% strand | P13100 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 4 copies · chains A, B, C, D
- F89 · S)-2-(5(((1,2-dihydro-3-methyl-1-oxobenzo(f)quinazolin-9-yl)methyl)amino)1-oxo-2-isoindolinyl)glutaric acid · ligand · 4 copies · chains A, B, C, 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 591 | 0.80 | 0.86 | 70 | UMP, F89 |
| 2 | 469 | 0.80 | 0.87 | 48 | UMP, F89 |
| 3 | 961 | 0.79 | 0.81 | 108 | empty |
| 4 | 437 | 0.78 | 0.87 | 52 | UMP, F89 |
| 5 | 452 | 0.78 | 0.86 | 47 | UMP, F89 |
Interfaces
5 interfaces between chains.
- A–B · 2105 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2101 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 348 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 38 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 29 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1F28 · Crystal structure of thymidylate synthase from pneumocystis carinii bound to dump and… · the same entry in another collection · chain D against D, TM-score 1.00
- P13100 · AlphaFold monomer V2.0 prediction for thymidylate synthase (P13100) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P13100
- Elsewhere: RCSB PDB 1F28 · PDBe 1F28 · UniProt P13100
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