Research workbench
HIF prolyl hydroxylase 2 (PHD2/EGLN1) R371H variant in complex with Mn(II) and N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine (IOX3/UN9)
Analyse HIF prolyl hydroxylase 2 (PHD2/EGLN1) R371H variant in complex with Mn(II) and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LB6
- Type
- protein
- Length
- 221 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.7
- Source
- Homo sapiens
- Molecule
- Egl nine homolog 1
- EC
- 1.14.11.29
- UniProt
- Q9GZT9
- Ligands
- UN9, MN, SO4
- Pockets
- 1 · best druggability 0.64
Structure
x-ray diffraction · resolution 1.7 · 1 distinct chain · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Egl nine homolog 1 (EC 1.14.11.29) | protein | 221 | 29% helix, 29% strand | Q9GZT9 |
Ligands and binding sites
- UN9 · N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.64 | 0.87 | 23 | MN, UN9 |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5LB6 · Hif prolyl hydroxylase 2 (PHD2/EGLN1) R371H variant in complex with MN(II) and… · 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 0.92
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
- Elsewhere: RCSB PDB 5LB6 · PDBe 5LB6 · UniProt Q9GZT9
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