Research workbench
Hif prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with N-oxalylglycine (nog)
Analyse Hif prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with N-oxalylglycine (nog) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L9R
- Type
- protein
- Length
- 220 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Egl nine homolog 1
- EC
- 1.14.11.29
- UniProt
- Q9GZT9
- Ligands
- OGA, MN, SO4
- Pockets
- 1 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Egl nine homolog 1 (EC 1.14.11.29) | protein | 220 | 31% helix, 31% strand | Q9GZT9 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 2 copies · chains A
- MN · Manganese (II) ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- PG4 · Tetraethylene glycol · additive · 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 | 119 | 0.68 | 0.90 | 25 | OGA |
Compared structures
- 5L9R · HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with N-oxalylglycine (NOG) · 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 0.97
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 5L9R · PDBe 5L9R · UniProt Q9GZT9
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