MolNFT v1 · #128991 · protein
Crystal structure of human RAB1B covalently bound to the gef domain of DRRA/SIDM from legionella pneumophila in the presence of GDP
5O74 · Multifunctional virulence effector protein drra: “Crystal structure of human RAB1B covalently bound to the gef domain of DRRA/SIDM from legionella pneumophila…”. X-ray diffraction, 1 ligand (GDP), 20 pockets (best druggability…
- PDB
- 5O74
- Type
- protein
- Length
- 2,132 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Multifunctional virulence effector protein drra; RAS-related protein rab-1B
- EC
- 2.7.7.-
- UniProt
- Q29ST3, Q9H0U4
- Ligands
- GDP
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 9 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Multifunctional virulence effector protein drra (EC 2.7.7.-) | protein | 191 | 68% helix, 3% strand | Q29ST3 |
| B, H | RAS-related protein rab-1B | protein | 170 | 36% helix, 26% strand | Q9H0U4 |
| C, G | Multifunctional virulence effector protein drra (EC 2.7.7.-) | protein | 192 | 66% helix, 2% strand | Q29ST3 |
| D | RAS-related protein rab-1B | protein | 161 | 34% helix, 28% strand | Q9H0U4 |
| F | RAS-related protein rab-1B | protein | 165 | 38% helix, 27% strand | Q9H0U4 |
| I | Multifunctional virulence effector protein drra (EC 2.7.7.-) | protein | 193 | 65% helix, 2% strand | Q29ST3 |
| J | RAS-related protein rab-1B | protein | 164 | 38% helix, 27% strand | Q9H0U4 |
| K | Multifunctional virulence effector protein drra (EC 2.7.7.-) | protein | 191 | 66% helix, 2% strand | Q29ST3 |
| L | RAS-related protein rab-1B | protein | 152 | 34% helix, 29% strand | Q9H0U4 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 6 copies · chains B, D, F, H, J, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 903 | 0.79 | 0.81 | 84 | empty |
| 2 | 946 | 0.79 | 0.81 | 81 | empty |
| 3 | 976 | 0.72 | 0.76 | 90 | empty |
| 4 | 890 | 0.72 | 0.76 | 75 | empty |
| 5 | 133 | 0.64 | 0.87 | 24 | empty |
Interfaces
23 interfaces between chains.
- A–B · 1789 Ų buried · 38 hydrogen bonds · protein-protein
- I–J · 1780 Ų buried · 38 hydrogen bonds · protein-protein
- G–H · 1750 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 1711 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 1652 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (nonstandard).
Compared structures
- 5O74 · Crystal structure of human Rab1b covalently bound to the GEF domain of DrrA/SidM from… · the same entry in another collection · chain L against L, TM-score 1.00
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 Q9H0U4
- Elsewhere: RCSB PDB 5O74 · PDBe 5O74 · UniProt Q29ST3 · UniProt Q9H0U4
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