Research workbench
Crystal structure of P24DELTA1 gold domain (native 1)
Analyse Crystal structure of P24DELTA1 gold domain (native 1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AZX
- Type
- protein
- Length
- 390 residues
- Chains
- 4
- 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 0.67
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 61% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Transmembrane EMP24 domain-containing protein 10 | protein | 100 | 3% helix, 60% strand | Q63584 |
| B | Transmembrane EMP24 domain-containing protein 10 | protein | 99 | 3% helix, 61% strand | Q63584 |
| D | Transmembrane EMP24 domain-containing protein 10 | protein | 91 | 0% helix, 63% strand | Q63584 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.67 | 0.78 | 66 | SO4 |
| 2 | 395 | 0.65 | 0.79 | 45 | SO4 |
Interfaces
6 interfaces between chains.
- A–B · 894 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 847 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 441 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 410 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 97 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5AZX · Crystal structure of p24delta1 GOLD domain (native 1) · 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 D 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 5AZX · PDBe 5AZX · UniProt Q63584
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