MolNFT v1 · #171173 · protein
Hif prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with md-253
6YVT · Egl nine homolog 1: “Hif prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with md-253”. X-ray diffraction, 3 ligands (PW2, MN, SO4), 10 pockets (best druggability 0.70). MolNFT v1 #171173 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6YVT
- Type
- protein
- Length
- 1,182 residues
- Chains
- 6
- 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
- PW2, MN, SO4
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 32% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Egl nine homolog 1 (EC 1.14.11.29) | protein | 197 | 32% helix, 32% strand | Q9GZT9 |
| B | Egl nine homolog 1 (EC 1.14.11.29) | protein | 199 | 32% helix, 33% strand | Q9GZT9 |
| C | Egl nine homolog 1 (EC 1.14.11.29) | protein | 196 | 32% helix, 32% strand | Q9GZT9 |
| D | Egl nine homolog 1 (EC 1.14.11.29) | protein | 199 | 32% helix, 31% strand | Q9GZT9 |
| E | Egl nine homolog 1 (EC 1.14.11.29) | protein | 194 | 32% helix, 31% strand | Q9GZT9 |
Ligands and binding sites
- PW2 · 2-[[5-(6-methoxynaphthalen-2-yl)-3-oxidanyl-pyridin-2-yl]carbonylamino]ethanoic acid · ligand · 6 copies · chains A, C, B, F, D, E
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · chains E
- GOL · Glycerol · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.70 | 0.90 | 25 | MN, PW2 |
| 2 | 309 | 0.69 | 0.83 | 40 | MN, PW2 |
| 3 | 320 | 0.68 | 0.82 | 41 | MN, PW2 |
| 4 | 282 | 0.66 | 0.82 | 38 | MN, PW2 |
| 5 | 264 | 0.64 | 0.81 | 35 | MN, PW2 |
Interfaces
9 interfaces between chains.
- B–E · 415 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 400 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 367 Ų buried · 3 hydrogen bonds · protein-protein
- B–F · 366 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 338 Ų buried · 3 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 6YVT · PDBe 6YVT · UniProt Q9GZT9
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