Research workbench
Mycobacterium tuberculosis dihydrofolate reductase complexed with trimetrexate (tmq)
Analyse Mycobacterium tuberculosis dihydrofolate reductase complexed with trimetrexate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M2X
- 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
- P0A546
- Ligands
- NDP, TMQ, PO4
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Dihydrofolate reductase (EC 1.5.1.3) | protein | 159 | 21% helix, 34% strand | P0A546 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, C, E, G
- TMQ · Trimetrexate · ligand · 4 copies · chains A, C, E, G
- PO4 · Phosphate ion · ion · chains A
- ACT · Acetate ion · additive · 22 copies · chains A, G, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 778 | 0.76 | 0.80 | 74 | NDP, TMQ, ACT, PO4 |
| 2 | 521 | 0.73 | 0.81 | 49 | NDP, TMQ, ACT |
| 3 | 469 | 0.72 | 0.82 | 48 | NDP, TMQ, ACT |
| 4 | 441 | 0.71 | 0.81 | 48 | NDP, TMQ, ACT |
| 5 | 233 | 0.52 | 0.76 | 34 | ACT |
Interfaces
3 interfaces between chains.
- E–G · 405 Ų buried · 6 hydrogen bonds · protein-protein
- A–G · 373 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 42 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4M2X · Mycobacterium tuberculosis dihydrofolate reductase complexed with trimetrexate (TMQ) · 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 P0A546
- Elsewhere: RCSB PDB 4M2X · PDBe 4M2X · UniProt P0A546
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