Research workbench
Crystal structure of CCM3, a cerebral cavernous malformation protein critical for vascular integrity
Analyse Crystal structure of CCM3, a cerebral cavernous malformation protein critical… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L8I
- Type
- protein
- Length
- 814 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Programmed cell death protein 10
- UniProt
- Q9BUL8
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Programmed cell death protein 10 | protein | 198 | 79% helix, 0% strand | Q9BUL8 |
| B | Programmed cell death protein 10 | protein | 201 | 81% helix, 0% strand | Q9BUL8 |
| C | Programmed cell death protein 10 | protein | 212 | 78% helix, 0% strand | Q9BUL8 |
| D | Programmed cell death protein 10 | protein | 203 | 81% helix, 0% strand | Q9BUL8 |
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.72 | 0.81 | 47 | empty |
| 2 | 653 | 0.66 | 0.75 | 53 | empty |
| 3 | 482 | 0.63 | 0.76 | 42 | empty |
| 4 | 278 | 0.53 | 0.75 | 34 | empty |
| 5 | 183 | 0.49 | 0.76 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1971 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1939 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 666 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 394 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 214 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3L8I · Crystal structure of CCM3, a cerebral cavernous malformation protein critical for… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9BUL8 · AlphaFold monomer V2.0 prediction for programmed cell death protein 10 (Q9BUL8) · a predicted model of the same protein · chain A against A, TM-score 0.68
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 Q9BUL8
- Elsewhere: RCSB PDB 3L8I · PDBe 3L8I · UniProt Q9BUL8
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