Research workbench
Crystal structure of GYP1 tbc domain in complex with RAB33 GTPase bound to GDP and ALF3
Analyse Crystal structure of GYP1 tbc domain in complex with RAB33 GTPase bound to GDP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2G77
- Type
- protein
- Length
- 504 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase-activating protein GYP1; RAS-related protein rab-33B
- UniProt
- Q08484, O35963
- Ligands
- GDP, AF3, MG
- Pockets
- 9 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase-activating protein GYP1 | protein | 331 | 69% helix, 1% strand | Q08484 |
| B | RAS-related protein rab-33B | protein | 173 | 37% helix, 25% strand | O35963 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A, B
- AF3 · Aluminum fluoride · ligand · chains A, B
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 339 | 0.58 | 0.76 | 35 | empty |
| 2 | 170 | 0.56 | 0.81 | 34 | MG, GDP, AF3 |
| 3 | 109 | 0.46 | 0.79 | 16 | empty |
| 4 | 184 | 0.45 | 0.75 | 27 | empty |
| 5 | 109 | 0.41 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1359 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 2G77 · Crystal Structure of Gyp1 TBC domain in complex with Rab33 GTPase bound to GDP and AlF3 · the same entry in another collection · chain A against A, TM-score 1.00
- Q08484 · AlphaFold monomer V2.0 prediction for GTPase-activating protein GYP1 (Q08484) · a predicted model of the same protein · chain A against A, TM-score 0.98
- O35963 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-33B (O35963) · a predicted model of the same protein · chain B 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 Q08484
- Every structure of UniProt O35963
- Elsewhere: RCSB PDB 2G77 · PDBe 2G77 · UniProt Q08484 · UniProt O35963
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