MolNFT v1 · #159268 · protein
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-L-glutamic acid
6OJV · Thymidylate SYNTHASE,THYMIDYLATE synthase: “Crystal structure of human thymidylate synthase DELTA(7-29) in complex with dump and…”. X-ray diffraction, 2 ligands (UMP, 2XB), 8 pockets (best druggability 0.82). MolNFT v1 #159268 on…
- PDB
- 6OJV
- 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, 2XB
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 34% 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 | 34% helix, 23% strand | P04818 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 4 copies · chains B, A, D, C
- 2XB · N-{4-[(2-amino-4-hydroxy-7H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzoyl}-L-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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 872 | 0.82 | 0.84 | 79 | UMP, 2XB |
| 2 | 316 | 0.77 | 0.88 | 39 | UMP, 2XB |
| 3 | 397 | 0.75 | 0.85 | 45 | UMP, 2XB |
| 4 | 357 | 0.73 | 0.85 | 44 | UMP, 2XB |
| 5 | 764 | 0.69 | 0.76 | 60 | empty |
Interfaces
4 interfaces between chains.
- A–D · 2165 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 305 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 199 Ų buried · 1 hydrogen bond · protein-protein
- B–A · 117 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6OJV · 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 6OJV · PDBe 6OJV · UniProt P04818
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