Research workbench
The complex structure of C3CER exoenzyme and GDP bound rhoa (NADH- bound state)
Analyse The complex structure of C3CER exoenzyme and GDP bound rhoa (NADH- bound state) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BWM
- Type
- protein
- Length
- 382 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transforming protein rhoa; ADP-ribosyltransferase
- UniProt
- P61586, Q8KNY0
- Ligands
- GDP, NAI, MG
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transforming protein rhoa | protein | 177 | 39% helix, 24% strand | P61586 |
| B | ADP-ribosyltransferase | protein | 205 | 30% helix, 27% strand | Q8KNY0 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · chains A, B
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 619 | 0.76 | 0.82 | 52 | NAI, EDO |
| 2 | 100 | 0.75 | 0.96 | 23 | empty |
| 3 | 310 | 0.58 | 0.77 | 49 | GDP, MG |
| 4 | 118 | 0.44 | 0.77 | 31 | empty |
| 5 | 52 | 0.26 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1069 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5BWM · The complex structure of C3cer exoenzyme and GDP bound RhoA (NADH-bound state) · the same entry in another collection · chain A against A, TM-score 1.00
- P61586 · AlphaFold monomer V2.0 prediction for transforming protein rhoa (P61586) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P61586
- Every structure of UniProt Q8KNY0
- Elsewhere: RCSB PDB 5BWM · PDBe 5BWM · UniProt P61586 · UniProt Q8KNY0
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