MolNFT v1 · #108627 · protein
Crystal structure of tripeptide bound cell shape determinant CSD4 protein from helicobacter pylori
4WCN · Conserved hypothetical secreted protein: “Crystal structure of tripeptide bound cell shape determinant CSD4 protein from helicobacter pylori”. X-ray diffraction, 4 ligands (3KS, NA, ZN), 4 pockets (best druggability 0.57). MolNFT v1…
- 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
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