Research workbench
Crystal structure of a gef domain from the orientia tsutsugamushi protein otdub in complex with RAC1
Analyse Crystal structure of a gef domain from the orientia tsutsugamushi protein otdub… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X1G
- Type
- protein
- Length
- 788 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ULP_PROTEASE domain-containing protein; RAS-related C3 botulinum toxin substrate 1
- EC
- 3.6.5.2
- UniProt
- B3CVM3, P63000
- Ligands
- MG
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | ULP_PROTEASE domain-containing protein | protein | 216 | 71% helix, 1% strand | B3CVM3 |
| B, D | RAS-related C3 botulinum toxin substrate 1 (EC 3.6.5.2) | protein | 178 | 41% helix, 22% strand | P63000 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.80 | 0.97 | 26 | MG |
| 2 | 115 | 0.78 | 0.97 | 29 | empty |
| 3 | 412 | 0.61 | 0.76 | 51 | empty |
| 4 | 307 | 0.58 | 0.77 | 48 | empty |
| 5 | 138 | 0.56 | 0.82 | 25 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1964 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 1906 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 597 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6X1G · Crystal structure of a GEF domain from the Orientia tsutsugamushi protein OtDUB in… · the same entry in another collection · chain A against A, 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 B3CVM3
- Every structure of UniProt P63000
- Elsewhere: RCSB PDB 6X1G · PDBe 6X1G · UniProt B3CVM3 · UniProt P63000
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