MolNFT v1 · #69773 · protein
Complex structure of SIDM/DRRA with the wild type RAB1
3L0I: “Complex structure of SIDM/DRRA with the wild type RAB1”. X-ray diffraction, 2 ligands (SO4, CL), 6 pockets (best druggability 0.85). MolNFT v1 #69773 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3L0I
- Type
- protein
- Length
- 974 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Drra; RAS-related protein rab-1A
- UniProt
- Q29ST3, P62820
- Ligands
- SO4, CL
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Drra | protein | 316 | 67% helix, 2% strand | Q29ST3 |
| B | RAS-related protein rab-1A | protein | 162 | 21% helix, 21% strand | P62820 |
| C | Drra | protein | 322 | 69% helix, 3% strand | Q29ST3 |
| D | RAS-related protein rab-1A | protein | 174 | 35% helix, 25% strand | P62820 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 978 | 0.85 | 0.86 | 105 | empty |
| 2 | 243 | 0.73 | 0.88 | 34 | empty |
| 3 | 223 | 0.49 | 0.75 | 34 | SO4 |
| 4 | 192 | 0.46 | 0.75 | 32 | empty |
| 5 | 69 | 0.33 | 0.76 | 15 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1854 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 1816 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 762 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 227 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 117 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified, 1 disulfide (engineered, disulfide).
Compared structures
- 3L0I · Complex structure of SidM/DrrA with the wild type Rab1 · the same entry in another collection · chain D against D, TM-score 1.00
- Q29ST3 · AlphaFold monomer V2.0 prediction for multifunctional virulence effector protein drra… · a predicted model of the same protein · chain A against A, TM-score 0.96
- P62820 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-1A (P62820) · a predicted model of the same protein · chain B against A, TM-score 0.76
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 Q29ST3
- Every structure of UniProt P62820
- Elsewhere: RCSB PDB 3L0I · PDBe 3L0I · UniProt Q29ST3 · UniProt P62820
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