Research workbench
Mycobacterium tuberculosis dihydrofolate reductase in complex with 3- ((thiophen-2-YLTHIO)METHYL)BENZOIC acid (fragment 13)
Analyse Mycobacterium tuberculosis dihydrofolate reductase in complex with 3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VSD
- 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
- JBB, NAP, CO, SO4, PO4
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydrofolate reductase (EC 1.5.1.3) | protein | 159 | 19% helix, 32% strand | P9WNX1 |
Ligands and binding sites
- JBB · 3-(thiophen-2-ylsulfanylmethyl)benzoic acid · ligand · 2 copies · chains A, B
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- CO · Cobalt (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- PO4 · Phosphate ion · ion · chains 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 | 532 | 0.73 | 0.81 | 50 | JBB, NAP |
| 2 | 553 | 0.73 | 0.81 | 42 | JBB, NAP |
| 3 | 233 | 0.65 | 0.83 | 36 | empty |
| 4 | 83 | 0.47 | 0.82 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 805 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6VSD · Mycobacterium tuberculosis dihydrofolate reductase in complex with… · 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 6VSD · PDBe 6VSD · UniProt P9WNX1
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