Research workbench
Inhibitor bound cell shape determinant protein CSD4 from helicobacter pylori
Analyse Inhibitor bound cell shape determinant protein CSD4 from helicobacter pylori in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D2R
- Type
- protein
- Length
- 420 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Conserved hypothetical secreted protein
- UniProt
- B5ZAD9
- Ligands
- 56W, ZN, IOD
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Conserved hypothetical secreted protein | protein | 420 | 24% helix, 32% strand | B5ZAD9 |
Ligands and binding sites
- 56W · (2R,6R)-2-{[(R)-[(3R)-3-(acetylamino)-3-carboxypropyl](hydroxy)phosphoryl]methyl}-6-aminoheptanedioic acid · ligand · chains A
- ZN · Zinc ion · metal · 3 copies · chains A
- IOD · Iodide ion · ion · 19 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 84 | 0.57 | 0.87 | 22 | 56W |
| 2 | 207 | 0.50 | 0.76 | 34 | IOD |
| 3 | 122 | 0.47 | 0.79 | 26 | IOD |
| 4 | 62 | 0.31 | 0.75 | 17 | empty |
Compared structures
- 5D2R · Inhibitor Bound Cell Shape Determinant Protein Csd4 from Helicobacter pylori · 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 B5ZAD9
- Elsewhere: RCSB PDB 5D2R · PDBe 5D2R · UniProt B5ZAD9
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