Research workbench
Crystal structure of human DHFR complexed with NADP and N10-formyl- tetrahydrofolate
Analyse Crystal structure of human DHFR complexed with NADP and N10-formyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SDB
- Type
- protein
- Length
- 372 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrofolate reductase
- EC
- 1.5.1.3
- UniProt
- P00374
- Ligands
- NAP, G3V
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydrofolate reductase (EC 1.5.1.3) | protein | 186 | 22% helix, 33% strand | P00374 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- G3V · N-(4-{[(2,4-diaminopteridin-6-yl) methyl](hydroxymethyl)amino}benzene-1-carbonyl)-L-glutamic acid · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 442 | 0.73 | 0.82 | 48 | NAP, G3V |
| 2 | 445 | 0.72 | 0.82 | 49 | NAP, G3V |
| 3 | 58 | 0.52 | 0.87 | 17 | empty |
| 4 | 215 | 0.52 | 0.77 | 40 | EDO |
Interfaces
1 interface between chains.
- A–B · 496 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5SDB · Crystal Structure of Human DHFR complexed with NADP and N10-formyl-tetrahydrofolate · the same entry in another collection · chain A against A, TM-score 1.00
- P00374 · AlphaFold monomer V2.0 prediction for dihydrofolate reductase (P00374) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P00374
- Elsewhere: RCSB PDB 5SDB · PDBe 5SDB · UniProt P00374
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