Research workbench
Moritella profunda dihydrofolate reductase (DHFR) in complex with NADPH and methotrexate (mtx)
Analyse Moritella profunda dihydrofolate reductase (DHFR) in complex with NADPH and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IA4
- Type
- protein
- Length
- 643 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrofolate reductase
- EC
- 1.5.1.3
- UniProt
- Q70YQ6
- Ligands
- NDP, MTX
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Dihydrofolate reductase (EC 1.5.1.3) | protein | 161 | 26% helix, 35% strand | Q70YQ6 |
| C | Dihydrofolate reductase (EC 1.5.1.3) | protein | 160 | 26% helix, 34% strand | Q70YQ6 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- MTX · Methotrexate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1153 | 0.84 | 0.85 | 99 | NDP, MTX |
| 2 | 340 | 0.69 | 0.82 | 42 | NDP, MTX |
| 3 | 351 | 0.69 | 0.82 | 45 | NDP, MTX |
| 4 | 71 | 0.46 | 0.82 | 21 | empty |
| 5 | 55 | 0.32 | 0.77 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 879 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 538 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 27 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3IA4 · Moritella profunda dihydrofolate reductase (DHFR) in complex with NADPH and methotrexate… · 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 Q70YQ6
- Elsewhere: RCSB PDB 3IA4 · PDBe 3IA4 · UniProt Q70YQ6
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