Research workbench
Crystal structure of Helicobacter pylori aminofutalosine deaminase (AFLDA) in complex with Methylthio-coformycin
Analyse Crystal structure of Helicobacter pylori aminofutalosine deaminase (AFLDA) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LKK
- Type
- protein
- Length
- 1,637 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.89
- Source
- Helicobacter pylori
- Molecule
- Aminofutalosine deaminase
- UniProt
- Q9ZMG8
- Ligands
- MCF, FE
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · resolution 1.89 · 3 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminofutalosine deaminase | protein | 411 | 38% helix, 25% strand | Q9ZMG8 |
| B, D | Aminofutalosine deaminase | protein | 409 | 39% helix, 25% strand | Q9ZMG8 |
| C | Aminofutalosine deaminase | protein | 408 | 39% helix, 25% strand | Q9ZMG8 |
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 · 4 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1148 | 0.79 | 0.80 | 110 | empty |
| 2 | 654 | 0.74 | 0.81 | 76 | EDO |
| 3 | 375 | 0.69 | 0.81 | 43 | MCF |
| 4 | 339 | 0.67 | 0.81 | 42 | MCF |
| 5 | 305 | 0.67 | 0.82 | 41 | MCF |
Interfaces
4 interfaces between chains.
- A–B · 1260 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1251 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 588 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 89 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7LKK · Crystal structure of helicobacter pylori aminofutalosine deaminase (aflda) in complex… · 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 Q9ZMG8
- Elsewhere: RCSB PDB 7LKK · PDBe 7LKK · UniProt Q9ZMG8
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