Research workbench
Human scbd (sorcin calcium binding domain) in complex with doxorubicin
Analyse Human scbd (sorcin calcium binding domain) in complex with doxorubicin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MRA
- Type
- protein
- Length
- 668 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sorcin
- UniProt
- P30626
- Ligands
- DM2, MG
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 59% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Sorcin | protein | 167 | 59% helix, 7% strand | P30626 |
Ligands and binding sites
- DM2 · Doxorubicin · ligand · chains A, B
- MG · Magnesium ion · metal · 10 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 978 | 0.80 | 0.81 | 76 | empty |
| 2 | 226 | 0.78 | 0.91 | 31 | empty |
| 3 | 336 | 0.77 | 0.88 | 47 | empty |
| 4 | 357 | 0.71 | 0.84 | 40 | empty |
| 5 | 152 | 0.61 | 0.85 | 37 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2016 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1989 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 941 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
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 P30626
- Elsewhere: RCSB PDB 5MRA · PDBe 5MRA · UniProt P30626
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