Research workbench
Crystal structure of leishmania major S-adenosylhomocysteine hydrolase
Analyse Crystal structure of leishmania major S-adenosylhomocysteine hydrolase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3G1U
- Type
- protein
- Length
- 1,666 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylhomocysteinase
- EC
- 3.3.1.1
- UniProt
- Q4Q124
- Ligands
- ADN, NAD
- Pockets
- 16 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 412 | 44% helix, 16% strand | Q4Q124 |
| C | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 424 | 43% helix, 15% strand | Q4Q124 |
| D | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 418 | 44% helix, 16% strand | Q4Q124 |
Ligands and binding sites
- ADN · Adenosine · ligand · 4 copies · chains A, B, C, D
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1061 | 0.87 | 0.88 | 66 | empty |
| 2 | 831 | 0.83 | 0.86 | 89 | ADN, NAD |
| 3 | 853 | 0.79 | 0.82 | 89 | ADN, NAD |
| 4 | 853 | 0.77 | 0.80 | 89 | empty |
| 5 | 810 | 0.77 | 0.81 | 87 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2201 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1925 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1911 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1900 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 492 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3G1U · Crystal structure of Leishmania major S-adenosylhomocysteine hydrolase · 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 Q4Q124
- Elsewhere: RCSB PDB 3G1U · PDBe 3G1U · UniProt Q4Q124
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