MolNFT v1 · #16003 · protein
Crystal structure of the traffic ATPase of the helicobacter pylori type IV secretion system in complex with atpgammas
1NLY · VIRB11 homolog: “Crystal structure of the traffic ATPase of the helicobacter pylori type IV secretion system in complex with…”. X-ray diffraction, 3 ligands (AGS, MG, SO4), 6 pockets (best druggability 0.82). MolNFT v1 #16003 on…
- PDB
- 1NLY
- Type
- protein
- Length
- 646 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VIRB11 homolog
- UniProt
- Q7BK04
- Ligands
- AGS, MG, SO4
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | VIRB11 homolog | protein | 323 | 39% helix, 23% strand | Q7BK04 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains B
- 2PE · Nonaethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.82 | 0.83 | 91 | SO4, AGS |
| 2 | 680 | 0.71 | 0.78 | 63 | empty |
| 3 | 387 | 0.71 | 0.82 | 57 | MG, AGS |
| 4 | 50 | 0.38 | 0.81 | 14 | empty |
| 5 | 110 | 0.35 | 0.73 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1900 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 1NLY · Crystal structure of the traffic ATPase of the Helicobacter pylori type IV secretion… · the same entry in another collection · chain B against B, 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 Q7BK04
- Elsewhere: RCSB PDB 1NLY · PDBe 1NLY · UniProt Q7BK04
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