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Crystal structure of human thymidylate synthase delta (7-29) in complex with dump and 2-amino-4-oxo-4,7-dihydro-PYRROLO[2,3- D]PYRIMIDINE-methyl-phenyl-D-glutamic 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
- 6OJU
- Type
- protein
- Length
- 1,140 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate SYNTHASE,THYMIDYLATE synthase
- EC
- 2.1.1.45
- UniProt
- P04818
- Ligands
- UMP, D96
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C, D | Thymidylate SYNTHASE,THYMIDYLATE synthase (EC 2.1.1.45) | protein | 285 | 33% helix, 23% strand | P04818 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 4 copies · chains B, A, C, D
- D96 · N-{4-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}-D-glutamic acid · ligand · 4 copies · chains B, A, C, 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 | 743 | 0.75 | 0.80 | 72 | UMP, D96 |
| 2 | 687 | 0.75 | 0.81 | 67 | UMP, D96 |
| 3 | 667 | 0.75 | 0.81 | 57 | UMP, D96 |
| 4 | 657 | 0.74 | 0.80 | 58 | UMP, D96 |
| 5 | 92 | 0.38 | 0.76 | 17 | empty |
Interfaces
4 interfaces between chains.
- B–D · 306 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 294 Ų buried · 5 hydrogen bonds · protein-protein
- B–A · 142 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 138 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6OJU · Crystal structure of human thymidylate synthase Delta (7-29) in complex with dUMP and… · the same entry in another collection · chain B against B, 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 6OJU · PDBe 6OJU · UniProt P04818
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