MolNFT v1 · #111793 · protein
Structure of cadmium bound KDO8PS from H.PYLORI
4Z1C · 2-dehydro-3-deoxyphosphooctonate aldolase: “Structure of cadmium bound KDO8PS from H.PYLORI”. X-ray diffraction, 1 ligand (CD), 3 pockets (best druggability 0.75). MolNFT v1 #111793 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4Z1C
- Type
- protein
- Length
- 514 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
- CD
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 257 | 42% helix, 19% strand | P56060 |
Ligands and binding sites
- CD · Cadmium 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 492 | 0.75 | 0.83 | 47 | empty |
| 2 | 454 | 0.74 | 0.83 | 46 | empty |
| 3 | 139 | 0.65 | 0.87 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1465 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4Z1C · Structure of Cadmium 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 4Z1C · PDBe 4Z1C · UniProt P56060
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