Research workbench
Crystal structure of the RAB27A fusion with SLP2A-RBDA1 effector for SF4 pocket drug targeting
Analyse Crystal structure of the RAB27A fusion with SLP2A-RBDA1 effector for SF4 pocket… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OPP
- Type
- protein
- Length
- 419 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Synaptotagmin-like protein 2,RAS-related protein rab-27A
- EC
- 3.6.5.2
- UniProt
- Q9HCH5, P51159
- Ligands
- GNP, MG
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Synaptotagmin-like protein 2,RAS-related protein rab-27A (EC 3.6.5.2) | protein | 210 | 43% helix, 22% strand | Q9HCH5, P51159 |
| C | Synaptotagmin-like protein 2,RAS-related protein rab-27A (EC 3.6.5.2) | protein | 209 | 42% helix, 23% strand | Q9HCH5, P51159 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.70 | 0.94 | 24 | empty |
| 2 | 201 | 0.58 | 0.80 | 34 | GNP, MG |
| 3 | 208 | 0.57 | 0.80 | 39 | GNP, MG |
| 4 | 303 | 0.52 | 0.74 | 40 | empty |
| 5 | 89 | 0.32 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–C · 1482 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 7OPP · Crystal structure of the Rab27a fusion with Slp2a-RBDa1 effector for SF4 pocket drug… · the same entry in another collection · chain A against A, TM-score 1.00
- P51159 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-27A (P51159) · a predicted model of the same protein · chain C against A, TM-score 0.85
- Q9HCH5 · AlphaFold monomer V2.0 prediction for synaptotagmin-like protein 2 (Q9HCH5) · a predicted model of the same protein · chain C against A, TM-score 0.27
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 Q9HCH5
- Every structure of UniProt P51159
- Elsewhere: RCSB PDB 7OPP · PDBe 7OPP · UniProt Q9HCH5 · UniProt P51159
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