MolNFT v1 · #61315 · protein
Crystal structures of mycobacterium tuberculosis S-adenosyl-L- homocysteine hydrolase in ternary complex with substrate and inhibitors
3DHY · Adenosylhomocysteinase: “Crystal structures of mycobacterium tuberculosis S-adenosyl-L- homocysteine hydrolase in ternary complex with…”. X-ray diffraction, 2 ligands (3DH, NAD), 19 pockets (best druggability 0.87). MolNFT v1 #61315…
- PDB
- 3DHY
- Type
- protein
- Length
- 1,941 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylhomocysteinase
- EC
- 3.3.1.1
- UniProt
- P60176
- Ligands
- 3DH, NAD
- Pockets
- 19 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 486 | 46% helix, 15% strand | P60176 |
| B, C, D | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 485 | 44% helix, 14% strand | P60176 |
Ligands and binding sites
- 3DH · 5'-S-ethyl-5'-thioadenosine · ligand · 4 copies · chains A, B, C, D
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 680 | 0.87 | 0.92 | 70 | empty |
| 2 | 729 | 0.86 | 0.90 | 84 | 3DH, NAD |
| 3 | 641 | 0.86 | 0.91 | 82 | 3DH, NAD |
| 4 | 645 | 0.85 | 0.90 | 78 | 3DH, NAD |
| 5 | 1075 | 0.84 | 0.85 | 103 | 3DH, NAD |
Interfaces
6 interfaces between chains.
- A–B · 3351 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 3342 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 1864 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 1860 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 507 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3DHY · Crystal Structures of Mycobacterium tuberculosis S-Adenosyl-L-Homocysteine Hydrolase in… · 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 P60176
- Elsewhere: RCSB PDB 3DHY · PDBe 3DHY · UniProt P60176
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