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Crystal structure of human Rab38 in complex with GTP
Analyse Crystal structure of human Rab38 in complex with GTP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HDU
- Type
- protein
- Length
- 685 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.793
- Source
- Homo sapiens
- Molecule
- Ras-related protein Rab-38
- UniProt
- P57729
- Ligands
- GTP, MG
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · resolution 1.793 · 4 distinct chains · 34% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ras-related protein Rab-38 | protein | 172 | 34% helix, 30% strand | P57729 |
| B | Ras-related protein Rab-38 | protein | 170 | 32% helix, 30% strand | P57729 |
| C | Ras-related protein Rab-38 | protein | 170 | 34% helix, 31% strand | P57729 |
| D | Ras-related protein Rab-38 | protein | 173 | 36% helix, 29% strand | P57729 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.76 | 0.79 | 87 | empty |
| 2 | 377 | 0.67 | 0.80 | 46 | GTP, MG |
| 3 | 155 | 0.55 | 0.81 | 28 | GTP, MG |
| 4 | 147 | 0.54 | 0.81 | 27 | GTP, MG |
| 5 | 149 | 0.53 | 0.80 | 28 | GTP, MG |
Interfaces
6 interfaces between chains.
- C–D · 611 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 484 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 375 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 245 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 89 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 P57729
- Elsewhere: RCSB PDB 6HDU · PDBe 6HDU · UniProt P57729
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