Research workbench
Crystal structure of human rhob-GTP in complex with nanobody B6
Analyse Crystal structure of human rhob-GTP in complex with nanobody B6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SGE
- Type
- protein
- Length
- 620 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rho-related GTP-binding protein rhob; Nanobody B6
- UniProt
- P62745, A0A4E0W6L3
- Ligands
- GTP, MG
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rho-related GTP-binding protein rhob | protein | 178 | 42% helix, 26% strand | P62745 |
| B | Nanobody B6 | protein | 126 | 6% helix, 41% strand | A0A4E0W6L3 |
| C | Rho-related GTP-binding protein rhob | protein | 182 | 40% helix, 25% strand | P62745 |
| D | Nanobody B6 | protein | 134 | 5% helix, 40% strand | A0A4E0W6L3 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 712 | 0.75 | 0.80 | 87 | empty |
| 2 | 236 | 0.70 | 0.86 | 38 | GTP, MG |
| 3 | 362 | 0.69 | 0.82 | 59 | GTP, MG |
| 4 | 318 | 0.66 | 0.81 | 43 | empty |
| 5 | 62 | 0.41 | 0.81 | 15 | empty |
Interfaces
5 interfaces between chains.
- B–C · 779 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 770 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 735 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 704 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 24 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6SGE · Crystal structure of Human RHOB-GTP in complex with nanobody B6 · the same entry in another collection · chain A against A, TM-score 1.00
- P62745 · AlphaFold monomer V2.0 prediction for rho-related GTP-binding protein rhob (P62745) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P62745
- Every structure of UniProt A0A4E0W6L3
- Elsewhere: RCSB PDB 6SGE · PDBe 6SGE · UniProt P62745 · UniProt A0A4E0W6L3
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