Research workbench
PHD2:MN:NOG:HIF1-alpha substrate complex
Analyse PHD2:MN:NOG:HIF1-alpha substrate complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HQR
- Type
- protein
- Length
- 242 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Egl nine homolog 1; Hypoxia-inducible factor 1 alpha
- EC
- 1.14.11.-
- UniProt
- Q9GZT9, Q16665
- Ligands
- OGA, MN
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Egl nine homolog 1 (EC 1.14.11.-) | protein | 225 | 30% helix, 30% strand | Q9GZT9 |
| S | Hypoxia-inducible factor 1 alpha | protein | 17 | 18% helix, 18% strand | Q16665 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.73 | 1.00 | 20 | MN, OGA |
| 2 | 62 | 0.31 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–S · 1210 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3HQR · PHD2:Mn:NOG:HIF1-alpha substrate complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q9GZT9 · AlphaFold monomer V2.0 prediction for egl nine homolog 1 (Q9GZT9) · a predicted model of the same protein · chain A against A, TM-score 0.96
- Q16665 · AlphaFold monomer V2.0 prediction for hypoxia-inducible factor 1-alpha (Q16665) · a predicted model of the same protein · chain S against A, TM-score 0.42
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 Q9GZT9
- Every structure of UniProt Q16665
- Elsewhere: RCSB PDB 3HQR · PDBe 3HQR · UniProt Q9GZT9 · UniProt Q16665
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