Research workbench
Mycobacterium tuberculosis dihydrofolate reductase complexed with beta-NADPH and 4-[3-[3-[2,4-BIS(AZANYL)-6-ethyl-pyrimidin-5-YL]PROP- 2-ynyl]-5-methoxy-PHENYL]BENZOIC acid
Analyse Mycobacterium tuberculosis dihydrofolate reductase complexed with beta-NADPH… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DDS
- Type
- protein
- Length
- 636 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrofolate reductase
- EC
- 1.5.1.3
- UniProt
- P9WNX1
- Ligands
- NDP, U75, NA
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Dihydrofolate reductase (EC 1.5.1.3) | protein | 159 | 21% helix, 33% strand | P9WNX1 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- U75 · 4-[3-[3-[2,4-bis(azanyl)-6-ethyl-pyrimidin-5-yl]prop-2-ynyl]-5-methoxy-phenyl]benzoic acid · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains A
- GOL · Glycerol · additive · 5 copies · chains B, C, D
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1068 | 0.80 | 0.82 | 93 | ACT, NDP, U75 |
| 2 | 519 | 0.71 | 0.80 | 49 | NDP, U75 |
| 3 | 509 | 0.71 | 0.80 | 49 | NDP, U75 |
| 4 | 490 | 0.70 | 0.80 | 46 | NDP, U75 |
| 5 | 148 | 0.43 | 0.75 | 21 | empty |
Interfaces
4 interfaces between chains.
- A–B · 563 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 550 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 288 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 178 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6DDS · Mycobacterium tuberculosis Dihydrofolate Reductase complexed with beta-NADPH and… · the same entry in another collection · chain D against D, TM-score 1.00
- P9WNX1 · AlphaFold monomer V2.0 prediction for dihydrofolate reductase (P9WNX1) · a predicted model of the same protein · chain A 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 6DDS · PDBe 6DDS · UniProt P9WNX1
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