MolNFT v1 · #111794 · protein
Structure of pep and zinc bound KDO8PS from H.PYLORI
4Z1D · 2-dehydro-3-deoxyphosphooctonate aldolase: “Structure of pep and zinc bound KDO8PS from H.PYLORI”. X-ray diffraction, 2 ligands (PEP, ZN), 3 pockets (best druggability 0.74). MolNFT v1 #111794 on GenesisL1: 3D structure, binding…
- PDB
- 4Z1D
- Type
- protein
- Length
- 512 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-dehydro-3-deoxyphosphooctonate aldolase
- EC
- 2.5.1.55
- UniProt
- P56060
- Ligands
- PEP, ZN
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 256 | 43% helix, 19% strand | P56060 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 535 | 0.74 | 0.82 | 56 | PEP |
| 2 | 489 | 0.74 | 0.83 | 50 | PEP |
| 3 | 64 | 0.35 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1560 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 4Z1D · Structure of PEP and zinc bound KDO8PS from H.pylori · the same entry in another collection · chain A against A, TM-score 1.00
- P56060 · AlphaFold monomer V2.0 prediction for 2-dehydro-3-deoxyphosphooctonate aldolase (P56060) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P56060
- Elsewhere: RCSB PDB 4Z1D · PDBe 4Z1D · UniProt P56060
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