Research workbench
Crystal structure of recombinant rat-liver D244E mutant S- adenosylhomocysteine hydrolase
Analyse Crystal structure of recombinant rat-liver D244E mutant S- adenosylhomocysteine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1D4F
- Type
- protein
- Length
- 1,720 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosylhomocysteine hydrolase
- EC
- 3.3.1.1
- UniProt
- P10760
- Ligands
- NAD, ADN
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | S-adenosylhomocysteine hydrolase (EC 3.3.1.1) | protein | 430 | 43% helix, 17% strand | P10760 |
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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 972 | 0.89 | 0.91 | 67 | empty |
| 2 | 764 | 0.86 | 0.89 | 75 | NAD, ADN |
| 3 | 736 | 0.85 | 0.88 | 79 | NAD, ADN |
| 4 | 728 | 0.85 | 0.88 | 80 | NAD, ADN |
| 5 | 929 | 0.85 | 0.86 | 98 | NAD, ADN |
Interfaces
6 interfaces between chains.
- C–D · 3134 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 3102 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 1798 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1719 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 453 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1D4F · Crystal structure of recombinant rat-liver D244E mutant S-adenosylhomocysteine hydrolase · the same entry in another collection · chain A against A, TM-score 1.00
- P10760 · AlphaFold monomer V2.0 prediction for adenosylhomocysteinase (P10760) · a predicted model of the same protein · chain A 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 P10760
- Elsewhere: RCSB PDB 1D4F · PDBe 1D4F · UniProt P10760
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