Research workbench
Klebsiella pneumoniae DFRA1 complexed with NADPH and 6-ethyl-5-(3-(2- methoxy-5-(pyridin-4-YL)PHENYL)PROP-1-yn-1-YL)PYRIMIDINE-2,4-diamine
Analyse Klebsiella pneumoniae DFRA1 complexed with NADPH and 6-ethyl-5-(3-(2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ECC
- Type
- protein
- Length
- 314 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dehydrofolate reductase type I
- UniProt
- A4GRC7
- Ligands
- 6DR, NAP, CA
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dehydrofolate reductase type I | protein | 157 | 24% helix, 37% strand | A4GRC7 |
Ligands and binding sites
- 6DR · 6-ethyl-5-{3-[2-methoxy-5-(pyridin-4-yl)phenyl]prop-1-yn-1-yl}pyrimidine-2,4-diamine · ligand · 4 copies · chains A, B
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 3 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 451 | 0.69 | 0.80 | 43 | NAP, 6DR |
| 2 | 417 | 0.68 | 0.80 | 43 | NAP, 6DR |
Interfaces
1 interface between chains.
- A–B · 1005 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5ECC · Klebsiella pneumoniae DfrA1 complexed with NADPH and… · 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 A4GRC7
- Elsewhere: RCSB PDB 5ECC · PDBe 5ECC · UniProt A4GRC7
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