MolNFT v1 · #65875 · protein
S-adenosyl homocysteine hydrolase (sahh) from trypanosoma brucei
3H9U · Adenosylhomocysteinase: “S-adenosyl homocysteine hydrolase (sahh) from trypanosoma brucei”. X-ray diffraction, 2 ligands (NAD, ADN), 19 pockets (best druggability 0.84). MolNFT v1 #65875 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3H9U
- Type
- protein
- Length
- 1,729 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylhomocysteinase
- EC
- 3.3.1.1
- UniProt
- Q383X0
- Ligands
- NAD, ADN
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 430 | 44% helix, 16% strand | Q383X0 |
| B | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 430 | 45% helix, 15% strand | Q383X0 |
| C | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 435 | 44% helix, 15% strand | Q383X0 |
| D | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 434 | 43% helix, 15% strand | Q383X0 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- ADN · Adenosine · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains C
- PG4 · Tetraethylene glycol · additive · chains 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 566 | 0.84 | 0.90 | 73 | NAD, ADN |
| 2 | 559 | 0.84 | 0.90 | 76 | NAD, ADN |
| 3 | 544 | 0.84 | 0.90 | 72 | NAD, ADN |
| 4 | 563 | 0.83 | 0.89 | 74 | NAD, ADN |
| 5 | 351 | 0.74 | 0.86 | 30 | empty |
Interfaces
4 interfaces between chains.
- A–B · 3431 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 3405 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 265 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 130 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3H9U · S-adenosyl homocysteine hydrolase (SAHH) from Trypanosoma brucei · 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 Q383X0
- Elsewhere: RCSB PDB 3H9U · PDBe 3H9U · UniProt Q383X0
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