Research workbench
The crystal structure of GBP1 with lrr domain of IPAH9.8
Analyse The crystal structure of GBP1 with lrr domain of IPAH9.8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K2D
- Type
- protein
- Length
- 642 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanylate-binding protein 1; E3 ubiquitin-protein ligase IPAH9.8
- EC
- 3.6.5.-, 2.3.2.27
- UniProt
- P32455, Q8VSC3
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanylate-binding protein 1 (EC 3.6.5.-) | protein | 428 | 51% helix, 9% strand | P32455 |
| B | E3 ubiquitin-protein ligase IPAH9.8 (EC 2.3.2.27) | protein | 214 | 16% helix, 14% strand | Q8VSC3 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 493 | 0.66 | 0.78 | 53 | empty |
| 2 | 361 | 0.59 | 0.76 | 29 | empty |
| 3 | 57 | 0.46 | 0.83 | 13 | empty |
| 4 | 149 | 0.45 | 0.76 | 27 | empty |
| 5 | 72 | 0.36 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 967 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6K2D · The crystal structure of GBP1 with LRR domain of IpaH9.8 · the same entry in another collection · chain A against A, TM-score 1.00
- Q8VSC3 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase IPAH9.8 (Q8VSC3) · a predicted model of the same protein · chain B against A, TM-score 0.95
- P32455 · AlphaFold monomer V2.0 prediction for guanylate-binding protein 1 (P32455) · a predicted model of the same protein · chain A against A, TM-score 0.84
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 P32455
- Every structure of UniProt Q8VSC3
- Elsewhere: RCSB PDB 6K2D · PDBe 6K2D · UniProt P32455 · UniProt Q8VSC3
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