MolNFT v1 · #56684 · protein
Crystal structure of ZN2+-bound form of DES3-23ALG-2 complexed with alix abs peptide
2ZNE · Programmed cell death protein 6: “Crystal structure of ZN2+-bound form of DES3-23ALG-2 complexed with alix abs peptide”. X-ray diffraction, 2 ligands (ZN, NA), 2 pockets (best druggability 0.37). MolNFT v1 #56684 on GenesisL1: 3D…
- PDB
- 2ZNE
- Type
- protein
- Length
- 362 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Programmed cell death protein 6; 16-meric peptide from programmed cell death…
- UniProt
- O75340, Q8WUM4
- Ligands
- ZN, NA
- Pockets
- 2 · best druggability 0.37
Structure
x-ray diffraction · 4 distinct chains · 55% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Programmed cell death protein 6 | protein | 168 | 60% helix, 7% strand | O75340 |
| B | Programmed cell death protein 6 | protein | 167 | 60% helix, 7% strand | O75340 |
| C | 16-meric peptide from programmed cell death 6-interacting protein | protein | 15 | 0% helix, 0% strand | Q8WUM4 |
| D | 16-meric peptide from programmed cell death 6-interacting protein | protein | 12 | 0% helix, 0% strand | Q8WUM4 |
Ligands and binding sites
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 | 100 | 0.37 | 0.75 | 16 | empty |
| 2 | 54 | 0.34 | 0.77 | 12 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1504 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 791 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 634 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 81 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2ZNE · Crystal structure of Zn2+-bound form of des3-23ALG-2 complexed with Alix ABS peptide · the same entry in another collection · chain D against D, TM-score 1.00
- O75340 · AlphaFold monomer V2.0 prediction for programmed cell death protein 6 (O75340) · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q8WUM4 · AlphaFold monomer V2.0 prediction for programmed cell death 6-interacting protein (Q8WUM4) · a predicted model of the same protein · chain C against A, TM-score 0.27
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 O75340
- Every structure of UniProt Q8WUM4
- Elsewhere: RCSB PDB 2ZNE · PDBe 2ZNE · UniProt O75340 · UniProt Q8WUM4
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