MolNFT v1 · #158222 · protein
Structure of closed state of dihydrofolate reductase from mycobacterium tuberculosis in complex with NADPH and pyrimethamine
6NNI: “Structure of closed state of dihydrofolate reductase from mycobacterium tuberculosis in complex with NADPH…”. X-ray diffraction, 4 ligands (NDP, CP6, CO), 4 pockets (best druggability 0.72). MolNFT v1 #158222 on GenesisL1: 3D…
- PDB
- 6NNI
- 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
- P9WNX1
- Ligands
- NDP, CP6, CO, SO4
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydrofolate reductase (EC 1.5.1.3) | protein | 159 | 19% helix, 35% strand | P9WNX1 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- CP6 · 5-(4-chloro-phenyl)-6-ethyl-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
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 571 | 0.72 | 0.80 | 50 | NDP, CP6, MES |
| 2 | 549 | 0.72 | 0.80 | 42 | NDP, CP6, MES |
| 3 | 50 | 0.59 | 0.93 | 20 | CO |
| 4 | 50 | 0.28 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 940 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6NNI · Structure of closed state of Dihydrofolate reductase from Mycobacterium tuberculosis in… · the same entry in another collection · chain A against A, TM-score 1.00
- P9WNX1 · AlphaFold monomer V2.0 prediction for dihydrofolate reductase (P9WNX1) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P9WNX1
- Elsewhere: RCSB PDB 6NNI · PDBe 6NNI · UniProt P9WNX1
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