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Crystal structure of SHANK3 spn domain in complex with GTP-bound RAP1B(G12V,Q63E)
Analyse Crystal structure of SHANK3 spn domain in complex with GTP-bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7C7J
- Type
- protein
- Length
- 511 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rap-1B; SH3 and multiple ankyrin repeat domains protein 3
- UniProt
- P61224, Q9BYB0
- Ligands
- GTP, MG, CA
- Pockets
- 8 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RAS-related protein rap-1B | protein | 167 | 35% helix, 28% strand | P61224 |
| C | SH3 and multiple ankyrin repeat domains protein 3 | protein | 89 | 24% helix, 35% strand | Q9BYB0 |
| D | SH3 and multiple ankyrin repeat domains protein 3 | protein | 88 | 24% helix, 35% strand | Q9BYB0 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 300 | 0.67 | 0.82 | 44 | GTP, MG |
| 2 | 337 | 0.67 | 0.81 | 47 | GTP |
| 3 | 185 | 0.53 | 0.78 | 30 | empty |
| 4 | 72 | 0.49 | 0.84 | 16 | empty |
| 5 | 152 | 0.47 | 0.77 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 622 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 566 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 532 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7C7J · Crystal structure of SHANK3 SPN domain in complex with GTP-bound Rap1b(G12V,Q63E) · the same entry in another collection · chain A against A, TM-score 1.00
- P61224 · AlphaFold monomer V2.0 prediction for RAS-related protein rap-1B (P61224) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9BYB0 · AlphaFold monomer V2.0 prediction for SH3 and multiple ankyrin repeat domains protein 3… · a predicted model of the same protein · chain D against A, TM-score 0.97
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 P61224
- Every structure of UniProt Q9BYB0
- Elsewhere: RCSB PDB 7C7J · PDBe 7C7J · UniProt P61224 · UniProt Q9BYB0
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