MolNFT v1 · #149825 · protein
Crystal structure of S-adenosyl-L-homocysteine hydrolase from cytophaga hutchinsonii in complex with adenosine
6GBN · Adenosylhomocysteinase: “Crystal structure of S-adenosyl-L-homocysteine hydrolase from cytophaga hutchinsonii in complex with adenosine”. X-ray diffraction, 3 ligands (ADN, NAD, NA), 11 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 6GBN
- Type
- protein
- Length
- 1,732 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylhomocysteinase
- EC
- 3.3.1.1
- UniProt
- Q11XG9
- Ligands
- ADN, NAD, NA
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 432 | 48% helix, 16% strand | Q11XG9 |
| B, D | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 435 | 48% helix, 16% strand | Q11XG9 |
| C | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 430 | 48% helix, 16% strand | Q11XG9 |
Ligands and binding sites
- ADN · Adenosine · ligand · 4 copies · chains A, B, C, D
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 619 | 0.85 | 0.90 | 73 | ADN, NAD |
| 2 | 584 | 0.85 | 0.90 | 70 | ADN, NAD |
| 3 | 621 | 0.84 | 0.89 | 73 | ADN, NAD |
| 4 | 653 | 0.84 | 0.89 | 82 | ADN, NAD |
| 5 | 391 | 0.72 | 0.84 | 31 | empty |
Interfaces
2 interfaces between chains.
- A–B · 3222 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 3185 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 6GBN · Crystal structure of S-adenosyl-L-homocysteine hydrolase from Cytophaga hutchinsonii 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
- Every structure of UniProt Q11XG9
- Elsewhere: RCSB PDB 6GBN · PDBe 6GBN · UniProt Q11XG9
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