MolNFT v1 · #125471 · protein
Hif prolyl hydroxylase 2 (PHD2-R281C/P317C) cross-linked to hif-1ALPHA nodd-L397C/D412C and N-oxalylglycine (nog) (complex-1)
5L9V · Egl nine homolog 1: “Hif prolyl hydroxylase 2 (PHD2-R281C/P317C) cross-linked to hif-1ALPHA nodd-L397C/D412C and N-oxalylglycine…”. X-ray diffraction, 2 ligands (OGA, MN), 5 pockets (best druggability 0.77). MolNFT v1 #125471 on…
- PDB
- 5L9V
- Type
- protein
- Length
- 468 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Egl nine homolog 1; Hypoxia-inducible factor 1-alpha
- EC
- 1.14.11.29
- UniProt
- Q9GZT9, Q16665
- Ligands
- OGA, MN
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Egl nine homolog 1 (EC 1.14.11.29) | protein | 215 | 29% helix, 32% strand | Q9GZT9 |
| C, D | Hypoxia-inducible factor 1-alpha | protein | 19 | 21% helix, 16% strand | Q16665 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 2 copies · chains A, C, B, D
- MN · Manganese (II) ion · metal · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.77 | 0.99 | 23 | MN, OGA |
| 2 | 73 | 0.76 | 0.99 | 20 | MN, OGA |
| 3 | 259 | 0.68 | 0.84 | 32 | empty |
| 4 | 217 | 0.51 | 0.76 | 22 | empty |
| 5 | 73 | 0.32 | 0.74 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1097 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1094 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 570 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 134 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 108 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5L9V · HIF prolyl hydroxylase 2 (PHD2-R281C/P317C) cross-linked to HIF-1alpha NODD-L397C/D412C… · 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 0.99
- Q16665 · AlphaFold monomer V2.0 prediction for hypoxia-inducible factor 1-alpha (Q16665) · a predicted model of the same protein · chain C against A, TM-score 0.32
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 5L9V · PDBe 5L9V · UniProt Q9GZT9 · UniProt Q16665
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