Research workbench
Crystal structure of the legionella pneumophila gap domain of lepb in complex with RAB1B bound to GDP and BEF3
Analyse Crystal structure of the legionella pneumophila gap domain of lepb in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I1O
- Type
- protein
- Length
- 1,831 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-1B; Lepb
- UniProt
- Q9H0U4, Q5ZSM7
- Ligands
- GDP, BEF, MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | RAS-related protein rab-1B | protein | 177 | 37% helix, 27% strand | Q9H0U4 |
| B | Lepb | protein | 280 | 59% helix, 3% strand | Q5ZSM7 |
| D, F, H | Lepb | protein | 281 | 58% helix, 3% strand | Q5ZSM7 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, D, B, C, E, F, G, H
- BEF · Beryllium trifluoride ion · ligand · 4 copies · chains A, D, B, C, E, F, G, H
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, E, F, G, H
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, C, B, D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 797 | 0.78 | 0.82 | 81 | GDP, BEF, PEG |
| 2 | 531 | 0.76 | 0.84 | 79 | empty |
| 3 | 573 | 0.74 | 0.82 | 68 | MG, GDP, BEF, PEG |
| 4 | 449 | 0.73 | 0.83 | 51 | empty |
| 5 | 292 | 0.72 | 0.86 | 45 | MG, GDP, BEF, PEG |
Interfaces
10 interfaces between chains.
- B–C · 1200 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1187 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 1179 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1171 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 451 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4I1O · Crystal structure of the Legionella pneumophila GAP domain of LepB in complex with Rab1b… · the same entry in another collection · chain H against H, TM-score 1.00
- Q9H0U4 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-1B (Q9H0U4) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9H0U4
- Every structure of UniProt Q5ZSM7
- Elsewhere: RCSB PDB 4I1O · PDBe 4I1O · UniProt Q9H0U4 · UniProt Q5ZSM7
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