MolNFT v1 · #121001 · protein
The high resolution structure of dihydrofolate reductase from yersinia pestis complex with methotrexate as closed form
5HI6: “The high resolution structure of dihydrofolate reductase from yersinia pestis complex with methotrexate as…”. X-ray diffraction, 4 ligands (MTX, K, CA), 3 pockets (best druggability 0.72). MolNFT v1 #121001 on GenesisL1: 3D…
- 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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