MolNFT v1 · #114030 · protein
Crystal structure of P24DELTA1 gold domain (native 2)
5AZY · Transmembrane EMP24 domain-containing protein 10: “Crystal structure of P24DELTA1 gold domain (native 2)”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.46). MolNFT v1 #114030 on GenesisL1: 3D structure, binding…
- PDB
- 5AZY
- Type
- protein
- Length
- 195 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transmembrane EMP24 domain-containing protein 10
- UniProt
- Q63584
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 61% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transmembrane EMP24 domain-containing protein 10 | protein | 97 | 3% helix, 61% strand | Q63584 |
| B | Transmembrane EMP24 domain-containing protein 10 | protein | 98 | 3% helix, 61% strand | Q63584 |
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 | 56 | 0.46 | 0.85 | 20 | EDO |
| 2 | 54 | 0.45 | 0.84 | 21 | SO4 |
Interfaces
1 interface between chains.
- A–B · 911 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5AZY · Crystal structure of p24delta1 GOLD domain (Native 2) · the same entry in another collection · chain A against A, TM-score 1.00
- Q63584 · AlphaFold monomer V2.0 prediction for transmembrane EMP24 domain- containing protein 10… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q63584
- Elsewhere: RCSB PDB 5AZY · PDBe 5AZY · UniProt Q63584
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