MolNFT v1 · #113053 · protein
Hif prolyl hydroxylase 2 (PHD2/EGLN1) in complex with 6-(5-oxo-4-(1H- 1,2,3-triazol-1-yl)-2,5-dihydro-1H-pyrazol-1-YL)NICOTINIC acid
5A3U · Egl nine homolog 1: “Hif prolyl hydroxylase 2 (PHD2/EGLN1) in complex with 6-(5-oxo-4-(1H…”. X-ray diffraction, 2 ligands (R8J, MN), 5 pockets (best druggability 0.78). MolNFT v1 #113053 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5A3U
- Type
- protein
- Length
- 616 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Egl nine homolog 1
- EC
- 1.14.11.2, 1.14.11.29, 1.14.11.-
- UniProt
- Q9GZT9
- Ligands
- R8J, MN
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Egl nine homolog 1 (EC 1.14.11.2, 1.14.11.29, 1.14.11.-) | protein | 215 | 29% helix, 30% strand | Q9GZT9 |
| B | Egl nine homolog 1 (EC 1.14.11.2, 1.14.11.29, 1.14.11.-) | protein | 202 | 26% helix, 30% strand | Q9GZT9 |
| C | Egl nine homolog 1 (EC 1.14.11.2, 1.14.11.29, 1.14.11.-) | protein | 199 | 29% helix, 29% strand | Q9GZT9 |
Ligands and binding sites
- R8J · 6-(5-oxo-4-(1H-1,2,3-triazol-1-yl)-2,5-dihydro-1H-pyrazol-1-yl)nicotinic acid · ligand · 3 copies · chains A, B, C
- MN · Manganese (II) ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 918 | 0.78 | 0.80 | 76 | MN, R8J |
| 2 | 150 | 0.58 | 0.82 | 19 | MN, R8J |
| 3 | 147 | 0.44 | 0.76 | 21 | empty |
| 4 | 104 | 0.36 | 0.74 | 20 | empty |
| 5 | 56 | 0.29 | 0.75 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1116 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 380 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 132 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 5A3U · PDBe 5A3U · UniProt Q9GZT9
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