Research workbench
Crystal structure of helicobacter pylori aminofutalosine deaminase (aflda)
Analyse Crystal structure of helicobacter pylori aminofutalosine deaminase (aflda) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LKJ
- Type
- protein
- Length
- 1,615 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminofutalosine deaminase
- UniProt
- Q9ZMG8
- Ligands
- FE
- Pockets
- 16 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Aminofutalosine deaminase | protein | 409 | 35% helix, 24% strand | Q9ZMG8 |
| B | Aminofutalosine deaminase | protein | 399 | 36% helix, 25% strand | Q9ZMG8 |
| D | Aminofutalosine deaminase | protein | 398 | 36% helix, 25% strand | Q9ZMG8 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 665 | 0.73 | 0.80 | 65 | empty |
| 2 | 423 | 0.71 | 0.82 | 43 | FE |
| 3 | 371 | 0.71 | 0.83 | 42 | FE |
| 4 | 451 | 0.70 | 0.81 | 51 | empty |
| 5 | 338 | 0.65 | 0.80 | 45 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1221 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1212 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 694 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 66 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 36 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7LKJ · Crystal structure of Helicobacter pylori aminofutalosine deaminase (AFLDA) · 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 7LKJ · PDBe 7LKJ · UniProt Q9ZMG8
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