Research workbench
Crystal-structure of the N-terminal large GTPase domain of human guanylate binding protein 1 (HGBP1) in complex with GMP/ALF4
Analyse Crystal-structure of the N-terminal large GTPase domain of human guanylate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2B8W
- Type
- protein
- Length
- 578 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interferon-induced guanylate-binding protein 1
- UniProt
- P32455
- Ligands
- ALF, 5GP, MG
- Pockets
- 4 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interferon-induced guanylate-binding protein 1 | protein | 288 | 39% helix, 22% strand | P32455 |
| B | Interferon-induced guanylate-binding protein 1 | protein | 290 | 39% helix, 21% strand | P32455 |
Ligands and binding sites
- ALF · Tetrafluoroaluminate ion · ligand · 2 copies · chains A, B
- 5GP · Guanosine-5'-monophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 579 | 0.88 | 0.94 | 86 | MG, ALF, 5GP |
| 2 | 215 | 0.49 | 0.75 | 33 | empty |
| 3 | 195 | 0.47 | 0.75 | 15 | empty |
| 4 | 155 | 0.42 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 2310 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 2B8W · Crystal-structure of the N-terminal Large GTPase Domain of human Guanylate Binding… · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.93
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
- Elsewhere: RCSB PDB 2B8W · PDBe 2B8W · UniProt P32455
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