Research workbench
Crystal structure of tripeptide bound cell shape determinant CSD4 protein from helicobacter pylori
Analyse Crystal structure of tripeptide bound cell shape determinant CSD4 protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WCN
- Type
- protein
- Length
- 414 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Conserved hypothetical secreted protein
- UniProt
- B5ZAD9
- Ligands
- 3KS, NA, ZN, IOD
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Conserved hypothetical secreted protein | protein | 414 | 25% helix, 33% strand | B5ZAD9 |
Ligands and binding sites
- 3KS · N-acetyl-L-alanyl-N-[(1S,5R)-5-amino-1,5-dicarboxypentyl]-D-glutamine · ligand · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- IOD · Iodide ion · ion · 41 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.57 | 0.85 | 22 | 3KS |
| 2 | 89 | 0.38 | 0.76 | 16 | IOD |
| 3 | 73 | 0.32 | 0.75 | 18 | IOD |
| 4 | 57 | 0.32 | 0.76 | 14 | empty |
Compared structures
- 4WCN · Crystal Structure of Tripeptide bound Cell Shape Determinant Csd4 protein from… · 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 4WCN · PDBe 4WCN · UniProt B5ZAD9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.