Research workbench
Structure of helicobacter pylori CSD6 in the D-ala-bound state
Analyse Structure of helicobacter pylori CSD6 in the D-ala-bound state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Y4V
- Type
- protein
- Length
- 632 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Conserved hypothetical secreted protein
- UniProt
- O25255
- Ligands
- DAL
- Pockets
- 10 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Conserved hypothetical secreted protein | protein | 316 | 29% helix, 36% strand | O25255 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.62 | 0.80 | 31 | empty |
| 2 | 249 | 0.55 | 0.77 | 28 | empty |
| 3 | 192 | 0.48 | 0.75 | 25 | empty |
| 4 | 173 | 0.48 | 0.76 | 24 | GOL |
| 5 | 50 | 0.47 | 0.86 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1139 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 4Y4V · Structure of Helicobacter pylori Csd6 in the D-Ala-bound state · 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 O25255
- Elsewhere: RCSB PDB 4Y4V · PDBe 4Y4V · UniProt O25255
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