MolNFT v1 · #148333 · protein
Crystal structure of S-adenosyl-L-homocysteine hydrolase from pseudomonas aeruginosa complexed with adenosine, K+ and ZN2+ cations
6F3M · Adenosylhomocysteinase: “Crystal structure of S-adenosyl-L-homocysteine hydrolase from pseudomonas aeruginosa complexed with…”. X-ray diffraction, 5 ligands (NAD, ADN, K), 20 pockets (best druggability 0.89). MolNFT v1 #148333 on…
- PDB
- 6F3M
- Type
- protein
- Length
- 1,841 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylhomocysteinase
- EC
- 3.3.1.1
- UniProt
- Q9I685
- Ligands
- NAD, ADN, K, ZN, PO4
- Pockets
- 20 · best druggability 0.89
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 | 461 | 47% helix, 15% strand | Q9I685 |
| B, C, D | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 460 | 47% helix, 15% strand | Q9I685 |
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
- K · Potassium ion · metal · 4 copies · chains A, C, B, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, C, B, D
- GOL · Glycerol · additive · 3 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1103 | 0.89 | 0.90 | 92 | empty |
| 2 | 568 | 0.84 | 0.89 | 76 | NAD, ADN |
| 3 | 587 | 0.84 | 0.89 | 70 | NAD, ADN, GOL |
| 4 | 593 | 0.83 | 0.89 | 77 | NAD, ADN |
| 5 | 796 | 0.83 | 0.86 | 100 | NAD, ADN, GOL |
Interfaces
6 interfaces between chains.
- C–D · 3211 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 3198 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 1900 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1896 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 451 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6F3M · Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9I685 · AlphaFold monomer V2.0 prediction for adenosylhomocysteinase (Q9I685) · a predicted model of the same protein · chain B 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 Q9I685
- Elsewhere: RCSB PDB 6F3M · PDBe 6F3M · UniProt Q9I685
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