Research workbench
Crystal structure of ts-DHFR from cryptosporidium hominis in complex with NADPH, fdump and 2-(4-((2-amino-4-oxo-4,7-dihydro-3H-PYRROLO[2, 3-D]PYRIMIDIN-5-YL)METHYL)BENZAMIDO)TEREPHTHALIC acid
Analyse Crystal structure of ts-DHFR from cryptosporidium hominis 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
- 6PF6
- Type
- protein
- Length
- 1,136 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, OEJ
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C | Thymidylate SYNTHASE,THYMIDYLATE synthase (EC 2.1.1.45) | protein | 285 | 33% helix, 24% strand | P04818 |
| A, D | Thymidylate SYNTHASE,THYMIDYLATE synthase (EC 2.1.1.45) | protein | 283 | 33% helix, 24% strand | P04818 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 4 copies · chains B, A, C, D
- OEJ · 2-({4-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}amino) benzene-1,4-dicarboxylic acid · ligand · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 450 | 0.77 | 0.85 | 56 | UMP, OEJ |
| 2 | 639 | 0.76 | 0.81 | 48 | empty |
| 3 | 374 | 0.73 | 0.84 | 43 | UMP, OEJ |
| 4 | 1030 | 0.72 | 0.76 | 88 | empty |
| 5 | 450 | 0.68 | 0.80 | 44 | UMP |
Interfaces
4 interfaces between chains.
- B–A · 2184 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 270 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 252 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 177 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6PF6 · Crystal structure of TS-DHFR from Cryptosporidium hominis in complex with NADPH, FdUMP… · 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 6PF6 · PDBe 6PF6 · UniProt P04818
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