Research workbench
Crystal structure of the 1ST SH3 domain from human CD2AP (cms) in complex with a proline-rich peptide (aa 378-393) from human RIN3
Analyse Crystal structure of the 1ST SH3 domain from human CD2AP (cms) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WCI
- Type
- protein
- Length
- 215 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CD2-associated protein; RAS and rab interactor 3
- UniProt
- Q9Y5K6, Q8TB24
- Ligands
- SO4
- Pockets
- 1 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 2% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CD2-associated protein | protein | 59 | 0% helix, 46% strand | Q9Y5K6 |
| B | RAS and rab interactor 3 | protein | 10 | 0% helix, 0% strand | Q8TB24 |
| C, E | CD2-associated protein | protein | 63 | 5% helix, 43% strand | Q9Y5K6 |
| D, F | RAS and rab interactor 3 | protein | 10 | 0% helix, 0% strand | Q8TB24 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.78 | 0.96 | 23 | SO4 |
Interfaces
6 interfaces between chains.
- E–F · 458 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 455 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 443 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 319 Ų buried · 0 hydrogen bonds · protein-protein
- C–E · 311 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4WCI · Crystal structure of the 1st SH3 domain from human CD2AP (CMS) in complex with a… · the same entry in another collection · chain F against F, TM-score 1.00
- Q9Y5K6 · AlphaFold monomer V2.0 prediction for CD2-associated protein (Q9Y5K6) · a predicted model of the same protein · chain A against A, TM-score 0.92
- Q8TB24 · AlphaFold monomer V2.0 prediction for RAS and rab interactor 3 (Q8TB24) · a predicted model of the same protein · chain B against A, TM-score 0.58
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 Q9Y5K6
- Every structure of UniProt Q8TB24
- Elsewhere: RCSB PDB 4WCI · PDBe 4WCI · UniProt Q9Y5K6 · UniProt Q8TB24
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