Research workbench
Crystal structure of dihydrofolate reductase from mycobacterium tuberculosis in complex with diaverdine
Analyse Crystal structure of dihydrofolate reductase from mycobacterium tuberculosis in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NNE
- Type
- protein
- Length
- 318 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrofolate reductase
- EC
- 1.5.1.3
- UniProt
- A5U6B6
- Ligands
- NDP, KUP, CO, SO4
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydrofolate reductase (EC 1.5.1.3) | protein | 159 | 20% helix, 33% strand | A5U6B6 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- KUP · 5-[(3,4-dimethoxyphenyl)methyl]pyrimidine-2,4-diamine · ligand · 2 copies · chains A, B
- CO · Cobalt (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 439 | 0.70 | 0.81 | 48 | NDP, KUP |
| 2 | 487 | 0.70 | 0.80 | 46 | NDP, KUP |
| 3 | 187 | 0.67 | 0.86 | 40 | empty |
| 4 | 52 | 0.29 | 0.75 | 15 | empty |
| 5 | 51 | 0.25 | 0.72 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 865 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6NNE · Crystal structure of Dihydrofolate reductase from Mycobacterium tuberculosis in 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 A5U6B6
- Elsewhere: RCSB PDB 6NNE · PDBe 6NNE · UniProt A5U6B6
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