MolNFT v1 · #29820 · protein
1.6 a crystal structure of a protein HP1531 of unknown function from helicobacter pylori
1ZKE · Hypothetical protein HP1531: “1.6 a crystal structure of a protein HP1531 of unknown function from helicobacter pylori”. X-ray diffraction, 1 ligand (MG), 2 pockets (best druggability 0.45). MolNFT v1 #29820 on GenesisL1: 3D…
- PDB
- 1ZKE
- Type
- protein
- Length
- 492 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein HP1531
- UniProt
- P64665
- Ligands
- MG
- Pockets
- 2 · best druggability 0.45
Structure
x-ray diffraction · 3 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hypothetical protein HP1531 | protein | 81 | 75% helix, 0% strand | P64665 |
| B, E | Hypothetical protein HP1531 | protein | 82 | 73% helix, 0% strand | P64665 |
| D, F | Hypothetical protein HP1531 | protein | 83 | 76% helix, 0% strand | P64665 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains B, F, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.45 | 0.80 | 22 | empty |
| 2 | 78 | 0.37 | 0.77 | 17 | MG |
Interfaces
9 interfaces between chains.
- B–F · 1483 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1437 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1413 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 343 Ų buried · 1 hydrogen bond · protein-protein
- C–E · 329 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1ZKE · 1.6 A Crystal Structure of a Protein HP1531 of Unknown Function from Helicobacter pylori · the same entry in another collection · chain F against F, TM-score 1.00
- P64665 · AlphaFold monomer V2.0 prediction for uncharacterized protein HP_1531 (P64665) · a predicted model of the same protein · chain D against A, TM-score 0.89
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 P64665
- Elsewhere: RCSB PDB 1ZKE · PDBe 1ZKE · UniProt P64665
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