Research workbench
Crystal structure of S-adenosyl-L-homocysteine hydrolase from bradyrhizobium elkanii in complex with adenosine
Analyse Crystal structure of S-adenosyl-L-homocysteine hydrolase from bradyrhizobium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LVC
- Type
- protein
- Length
- 1,872 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosyl-L-homocysteine hydrolase (sahase)
- EC
- 3.3.1.1
- Ligands
- NAD, ADN, NH4
- Pockets
- 16 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | S-adenosyl-L-homocysteine hydrolase (sahase) (EC 3.3.1.1) | protein | 468 | 47% helix, 14% strand | — |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- ADN · Adenosine · ligand · 3 copies · chains A, B, C
- NH4 · Ammonium ion · ion · 3 copies · chains A, C, B, D
- GOL · Glycerol · additive · 15 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 3 copies · chains 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1120 | 0.89 | 0.91 | 98 | GOL |
| 2 | 1158 | 0.84 | 0.84 | 123 | ADN, NAD, GOL, ACT |
| 3 | 1126 | 0.83 | 0.84 | 120 | ADN, NAD, GOL |
| 4 | 1064 | 0.83 | 0.84 | 120 | ADN, NAD, GOL |
| 5 | 1083 | 0.82 | 0.83 | 116 | NAD, GOL |
Interfaces
6 interfaces between chains.
- A–B · 3119 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 2992 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1788 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 1707 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 396 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4LVC · Crystal structure of S-adenosyl-L-homocysteine hydrolase from Bradyrhizobium elkanii 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
- Elsewhere: RCSB PDB 4LVC · PDBe 4LVC
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