MolNFT v1 · #29525 · protein
Structural basis of rab effector specificity: crystal structure of the small G protein RAB3A complexed with the effector domain of rabphilin-3A
1ZBD: “Structural basis of rab effector specificity: crystal structure of the small G protein RAB3A complexed with…”. X-ray diffraction, 3 ligands (GTP, ZN, MG), 4 pockets (best druggability 0.74). MolNFT v1 #29525 on GenesisL1: 3D…
- PDB
- 1ZBD
- Type
- protein
- Length
- 301 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rabphilin-3A
- UniProt
- P63012, P47709
- Ligands
- GTP, ZN, MG
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rabphilin-3A | protein | 177 | 37% helix, 27% strand | P63012 |
| B | Rabphilin-3A | protein | 124 | 41% helix, 11% strand | P47709 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 247 | 0.74 | 0.88 | 32 | empty |
| 2 | 188 | 0.55 | 0.79 | 33 | MG, GTP |
| 3 | 140 | 0.45 | 0.76 | 21 | empty |
| 4 | 78 | 0.30 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1498 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 modified (engineered).
Compared structures
- 1ZBD · Structural basis of rab effector specificity: crystal structure of the small G protein… · the same entry in another collection · chain A against A, TM-score 1.00
- P63012 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-3A (P63012) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P47709 · AlphaFold monomer V2.0 prediction for rabphilin-3A (P47709) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 P63012
- Every structure of UniProt P47709
- Elsewhere: RCSB PDB 1ZBD · PDBe 1ZBD · UniProt P63012 · UniProt P47709
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