Research workbench
Crystal structure of S-adenosyl-L-homocysteine hydrolase from brucella melitensis in ternary complex with NAD and adenosine, orthorhombic form
Analyse Crystal structure of S-adenosyl-L-homocysteine hydrolase from brucella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N58
- Type
- protein
- Length
- 1,843 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylhomocysteinase
- EC
- 3.3.1.1
- UniProt
- Q2YQX8
- Ligands
- NAD, ADN, K
- Pockets
- 15 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 460 | 47% helix, 15% strand | Q2YQX8 |
| B, C, D | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 461 | 47% helix, 15% strand | Q2YQX8 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- ADN · Adenosine · ligand · 3 copies · chains A, C, D
- K · Potassium ion · metal · 3 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 907 | 0.86 | 0.87 | 88 | empty |
| 2 | 730 | 0.83 | 0.87 | 82 | ADN, NAD |
| 3 | 1097 | 0.83 | 0.84 | 126 | ADN, NAD |
| 4 | 719 | 0.83 | 0.86 | 85 | ADN, NAD |
| 5 | 1085 | 0.82 | 0.83 | 118 | NAD |
Interfaces
6 interfaces between chains.
- C–D · 2969 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2912 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 1810 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 1600 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 393 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3N58 · Crystal structure of S-ADENOSYL-L-HOMOCYSTEINE hydrolase from brucella melitensis in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q2YQX8 · AlphaFold monomer V2.0 prediction for adenosylhomocysteinase (Q2YQX8) · a predicted model of the same protein · 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 Q2YQX8
- Elsewhere: RCSB PDB 3N58 · PDBe 3N58 · UniProt Q2YQX8
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