MolNFT v1 · #155154 · protein
Crystal structure of SHANK3 ntd-ank mutant in complex with RAP1
6KYK · SH3 and multiple ankyrin repeat domains protein 3: “Crystal structure of SHANK3 ntd-ank mutant in complex with RAP1”. X-ray diffraction, 2 ligands (GNP, MG), 20 pockets (best druggability 0.81). MolNFT v1 #155154 on GenesisL1: 3D…
- PDB
- 6KYK
- Type
- protein
- Length
- 1,390 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SH3 and multiple ankyrin repeat domains protein 3; RAS-related protein rap-1B
- UniProt
- Q4ACU6, P61224
- Ligands
- GNP, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SH3 and multiple ankyrin repeat domains protein 3 | protein | 359 | 41% helix, 10% strand | Q4ACU6 |
| B | SH3 and multiple ankyrin repeat domains protein 3 | protein | 357 | 41% helix, 10% strand | Q4ACU6 |
| C, E | RAS-related protein rap-1B | protein | 169 | 36% helix, 27% strand | P61224 |
| D, F | RAS-related protein rap-1B | protein | 168 | 36% helix, 27% strand | P61224 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 4 copies · chains C, D, E, F
- MG · Magnesium ion · metal · 4 copies · chains C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 908 | 0.81 | 0.83 | 77 | empty |
| 2 | 809 | 0.81 | 0.84 | 68 | empty |
| 3 | 990 | 0.79 | 0.80 | 99 | empty |
| 4 | 412 | 0.72 | 0.83 | 47 | GNP, MG |
| 5 | 404 | 0.71 | 0.82 | 45 | GNP |
Interfaces
5 interfaces between chains.
- A–B · 1360 Ų buried · 14 hydrogen bonds · protein-protein
- B–F · 1100 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1093 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 609 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 604 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6KYK · Crystal structure of Shank3 NTD-ANK mutant in complex with Rap1 · the same entry in another collection · chain F against F, TM-score 1.00
- Q4ACU6 · AlphaFold monomer V2.0 prediction for SH3 and multiple ankyrin repeat domains protein 3… · a predicted model of the same protein · chain B against A, TM-score 0.99
- P61224 · AlphaFold monomer V2.0 prediction for RAS-related protein rap-1B (P61224) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 Q4ACU6
- Every structure of UniProt P61224
- Elsewhere: RCSB PDB 6KYK · PDBe 6KYK · UniProt Q4ACU6 · UniProt P61224
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