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Crystal-structure of the N-terminal large GTPase domain of human guanylate binding protein 1 (HGBP1) in complex with gmp
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
- 2D4H
- Type
- protein
- Length
- 583 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
- 5GP
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interferon-induced guanylate-binding protein 1 | protein | 299 | 35% helix, 22% strand | P32455 |
| B | Interferon-induced guanylate-binding protein 1 | protein | 284 | 37% helix, 20% strand | P32455 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 551 | 0.77 | 0.83 | 80 | empty |
| 2 | 303 | 0.57 | 0.76 | 34 | 5GP |
| 3 | 250 | 0.54 | 0.76 | 31 | 5GP |
| 4 | 54 | 0.35 | 0.78 | 15 | empty |
| 5 | 55 | 0.32 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 866 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2D4H · 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 B against A, TM-score 0.90
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 2D4H · PDBe 2D4H · UniProt P32455
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