MolNFT v1 · #179463 · protein
Crystal structure of dihydrofolate reductase (DHFR) from mycobacterium abscessus atcc 19977 / dsm 44196 with NADP and inhibitor P218
7K6C: “Crystal structure of dihydrofolate reductase (DHFR) from mycobacterium abscessus atcc 19977 / dsm 44196 with…”. X-ray diffraction, 3 ligands (NAP, MMV, CA), 19 pockets (best druggability 0.74). MolNFT v1 #179463 on GenesisL1: 3D…
- PDB
- 7K6C
- Type
- protein
- Length
- 1,115 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrofolate reductase
- EC
- 1.5.1.3
- UniProt
- B1MD46
- Ligands
- NAP, MMV, CA
- Pockets
- 19 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, F | Dihydrofolate reductase (EC 1.5.1.3) | protein | 159 | 23% helix, 30% strand | B1MD46 |
| B, G | Dihydrofolate reductase (EC 1.5.1.3) | protein | 160 | 23% helix, 29% strand | B1MD46 |
| D | Dihydrofolate reductase (EC 1.5.1.3) | protein | 159 | 23% helix, 30% strand | B1MD46 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 7 copies · chains A, B, C, D, E, F, G
- MMV · 3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl) oxy]propoxy}phenyl)propanoic acid · ligand · 7 copies · chains A, B, C, D, E, F, G
- CA · Calcium ion · metal · 4 copies · chains A, C, B, E
- EDO · 1,2-ethanediol · additive · 6 copies · chains B, C, D, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 912 | 0.74 | 0.78 | 102 | NAP, MMV, EDO |
| 2 | 501 | 0.73 | 0.82 | 49 | NAP, MMV, EDO |
| 3 | 501 | 0.72 | 0.81 | 48 | NAP, MMV, EDO |
| 4 | 472 | 0.71 | 0.81 | 47 | NAP, MMV, EDO |
| 5 | 473 | 0.71 | 0.81 | 46 | NAP, MMV, EDO |
Interfaces
12 interfaces between chains.
- D–E · 375 Ų buried · 5 hydrogen bonds · protein-protein
- C–G · 358 Ų buried · 2 hydrogen bonds · protein-protein
- A–F · 313 Ų buried · 6 hydrogen bonds · protein-protein
- A–G · 273 Ų buried · 0 hydrogen bonds · protein-protein
- B–G · 255 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7K6C · Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium abscessus ATCC… · 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 B1MD46
- Elsewhere: RCSB PDB 7K6C · PDBe 7K6C · UniProt B1MD46
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