Research workbench
Crystal structure of human thymidylate synthase delta (7-29) in complex with dump and 2-(2-(4-((2-amino-4-oxo-4,7-dihydro-3H- PYRROLO[2,3-D]PYRIMIDIN-5-YL)METHYL)BENZAMIDO)-4-METHOXYPHENYL)ACETIC acid
Analyse Crystal structure of human thymidylate synthase delta (7-29) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PF5
- Type
- protein
- Length
- 1,140 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P04818
- Ligands
- UMP, OED
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Thymidylate synthase (EC 2.1.1.45) | protein | 285 | 34% helix, 24% strand | P04818 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 4 copies · chains A, B, C, D
- OED · [2-({4-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}amino)-4-methoxyphenyl]acetic 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
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 577 | 0.76 | 0.82 | 47 | UMP, OED |
| 2 | 598 | 0.75 | 0.82 | 49 | UMP, OED |
| 3 | 477 | 0.73 | 0.82 | 43 | UMP, OED |
| 4 | 473 | 0.73 | 0.82 | 42 | UMP, OED |
| 5 | 194 | 0.46 | 0.74 | 24 | empty |
Interfaces
4 interfaces between chains.
- C–D · 230 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 224 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 180 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 153 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6PF5 · Crystal structure of human thymidylate synthase Delta (7-29) in complex with dUMP and… · 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 P04818
- Elsewhere: RCSB PDB 6PF5 · PDBe 6PF5 · UniProt P04818
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