Research workbench
Hif prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with 2OG and rapid- derived silent allosteric cyclic peptide 3C (14-mer)
Analyse Hif prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with 2OG and rapid- derived… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YW1
- Type
- protein
- Length
- 222 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Egl nine homolog 1; PHD2-specific rapid cyclic peptide 3C (14-mer)
- EC
- 1.14.11.29
- UniProt
- Q9GZT9
- Ligands
- 48V, AKG, BCT, MN
- Pockets
- 1 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Egl nine homolog 1 (EC 1.14.11.29) | protein | 209 | 27% helix, 33% strand | Q9GZT9 |
| B | PHD2-specific rapid cyclic peptide 3C (14-mer) | protein | 13 | 0% helix, 23% strand | — |
Ligands and binding sites
- 48V · {[(2R)-2,3-diamino-3-oxopropyl]sulfanyl}acetic acid · ligand · chains A, B
- AKG · 2-oxoglutaric acid · ligand · chains A
- BCT · Bicarbonate ion · ligand · chains A
- MN · Manganese (II) ion · metal · 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 | 131 | 0.63 | 0.86 | 26 | MN, AKG |
Interfaces
1 interface between chains.
- A–B · 747 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 d-amino (covalent ligand, D-amino acid).
Compared structures
- 6YW1 · HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with 2OG and RaPID-derived silent… · 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 0.98
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 6YW1 · PDBe 6YW1 · UniProt Q9GZT9
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