MolNFT v1 · #106065 · protein
Structure of helicobacter pylori CSD3 from the hexagonal crystal
4RNZ · Conserved hypothetical secreted protein: “Structure of helicobacter pylori CSD3 from the hexagonal crystal”. X-ray diffraction, 3 ligands (NI, ZN, PO4), 4 pockets (best druggability 0.67). MolNFT v1 #106065 on GenesisL1: 3D…
- PDB
- 4RNZ
- Type
- protein
- Length
- 359 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Conserved hypothetical secreted protein
- UniProt
- O25247
- Ligands
- NI, ZN, PO4
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Conserved hypothetical secreted protein | protein | 359 | 19% helix, 41% strand | O25247 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- PO4 · Phosphate ion · ion · 3 copies · chains A
- GOL · Glycerol · additive · 3 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 | 413 | 0.67 | 0.80 | 50 | empty |
| 2 | 99 | 0.48 | 0.81 | 17 | empty |
| 3 | 137 | 0.42 | 0.75 | 31 | empty |
| 4 | 70 | 0.42 | 0.81 | 20 | empty |
Compared structures
- 4RNZ · Structure of Helicobacter pylori Csd3 from the hexagonal crystal · 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 O25247
- Elsewhere: RCSB PDB 4RNZ · PDBe 4RNZ · UniProt O25247
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