Research workbench
The high resolution structure of dihydrofolate reductase from yersinia pestis complex with methotrexate as closed form
Analyse The high resolution structure of dihydrofolate reductase from yersinia pestis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HI6
- Type
- protein
- Length
- 323 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrofolate reductase
- EC
- 1.5.1.3
- UniProt
- A0A0B6NYF5
- Ligands
- MTX, K, CA, CL
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydrofolate reductase (EC 1.5.1.3) | protein | 161 | 22% helix, 34% strand | A0A0B6NYF5 |
| B | Dihydrofolate reductase (EC 1.5.1.3) | protein | 162 | 24% helix, 33% strand | A0A0B6NYF5 |
Ligands and binding sites
- MTX · Methotrexate · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 812 | 0.72 | 0.78 | 48 | empty |
| 2 | 441 | 0.71 | 0.81 | 39 | MTX, K, CL |
| 3 | 445 | 0.66 | 0.78 | 40 | MTX |
Interfaces
1 interface between chains.
- A–B · 373 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 5HI6 · The high resolution structure of dihydrofolate reductase from Yersinia pestis complex… · 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 A0A0B6NYF5
- Elsewhere: RCSB PDB 5HI6 · PDBe 5HI6 · UniProt A0A0B6NYF5
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