Research workbench
Crystal structure of thymidylate synthase from pneumocystis carinii bound to dump and BW1843U89
Analyse Crystal structure of thymidylate synthase from pneumocystis carinii bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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