Research workbench
Cerebral cavernous malformation 3 (CCM3) in complex with paxillin LD2
Analyse Cerebral cavernous malformation 3 (CCM3) in complex with paxillin LD2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RQF
- Type
- protein
- Length
- 794 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Programmed cell death protein 10; Paxillin LD2 peptide
- UniProt
- Q9BUL8
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Programmed cell death protein 10 | protein | 197 | 79% helix, 0% strand | Q9BUL8 |
| B | Programmed cell death protein 10 | protein | 197 | 82% helix, 0% strand | Q9BUL8 |
| C | Programmed cell death protein 10 | protein | 197 | 83% helix, 0% strand | Q9BUL8 |
| D | Programmed cell death protein 10 | protein | 192 | 82% helix, 0% strand | Q9BUL8 |
| E | Paxillin LD2 peptide | protein | 11 | 82% helix, 0% strand | — |
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 584 | 0.71 | 0.79 | 54 | empty |
| 2 | 533 | 0.70 | 0.79 | 47 | empty |
| 3 | 624 | 0.64 | 0.75 | 54 | empty |
| 4 | 304 | 0.54 | 0.75 | 31 | empty |
| 5 | 144 | 0.47 | 0.77 | 31 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1984 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1969 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 704 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 508 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 403 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3RQF · Cerebral cavernous malformation 3 (CCM3) in complex with paxillin LD2 · the same entry in another collection · chain E against E, 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 3RQF · PDBe 3RQF · UniProt Q9BUL8
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