Research workbench
Crystal structure of dihydrofolate reductase from yersinia pestis complexed with methotrexate
Analyse Crystal structure of dihydrofolate reductase from yersinia pestis complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QI9
- Type
- protein
- Length
- 471 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrofolate reductase
- EC
- 1.5.1.3
- UniProt
- Q7CG83
- Ligands
- MTX
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydrofolate reductase (EC 1.5.1.3) | protein | 158 | 26% helix, 32% strand | Q7CG83 |
| B | Dihydrofolate reductase (EC 1.5.1.3) | protein | 159 | 24% helix, 32% strand | Q7CG83 |
| C | Dihydrofolate reductase (EC 1.5.1.3) | protein | 154 | 25% helix, 33% strand | Q7CG83 |
Ligands and binding sites
- MTX · Methotrexate · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 895 | 0.69 | 0.74 | 84 | MTX |
| 2 | 383 | 0.57 | 0.75 | 37 | empty |
| 3 | 196 | 0.49 | 0.75 | 23 | MTX |
| 4 | 77 | 0.31 | 0.74 | 15 | empty |
Interfaces
2 interfaces between chains.
- B–C · 927 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 180 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 4QI9 · Crystal structure of dihydrofolate reductase from Yersinia pestis complexed with… · 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 Q7CG83
- Elsewhere: RCSB PDB 4QI9 · PDBe 4QI9 · UniProt Q7CG83
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