MolNFT v1 · #92541 · protein
Crystal structure of adenosine deaminase from pseudomonas aeruginosa PAO1 with bound zn and methylthio-coformycin
4GBD · Putative uncharacterized protein: “Crystal structure of adenosine deaminase from pseudomonas aeruginosa PAO1 with bound zn and…”. X-ray diffraction, 3 ligands (MCF, ZN, PO4), 8 pockets (best druggability 0.77). MolNFT v1 #92541 on…
- PDB
- 4GBD
- Type
- protein
- Length
- 869 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein
- UniProt
- Q9HZ64
- Ligands
- MCF, ZN, PO4
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uncharacterized protein | protein | 435 | 44% helix, 24% strand | Q9HZ64 |
| B | Putative uncharacterized protein | protein | 434 | 44% helix, 24% strand | Q9HZ64 |
Ligands and binding sites
- MCF · (8R)-3-(5-S-methyl-5-thio-beta-D-ribofuranosyl)-3,6,7, 8-tetrahydroimidazo[4,5-d][1,3]diazepin-8-ol · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.77 | 0.98 | 27 | MCF |
| 2 | 90 | 0.76 | 0.97 | 25 | MCF |
| 3 | 472 | 0.72 | 0.83 | 61 | PO4 |
| 4 | 89 | 0.40 | 0.77 | 18 | empty |
| 5 | 101 | 0.39 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2290 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 4GBD · Crystal Structure Of Adenosine Deaminase From Pseudomonas Aeruginosa Pao1 with bound Zn… · 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 Q9HZ64
- Elsewhere: RCSB PDB 4GBD · PDBe 4GBD · UniProt Q9HZ64
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