Research workbench
Hif prolyl hydroxylase 2 (PHD2/EGLN1) in complex with tert-butyl 6-(5- hydroxy-4-(1H-1,2,3-triazol-1-yl)-1H-pyrazol-1-YL)NICOTINATE (IOX4)
Analyse Hif prolyl hydroxylase 2 (PHD2/EGLN1) in complex with tert-butyl 6-(5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZBN
- Type
- protein
- Length
- 1,196 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
- QEE, MN
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 29% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Egl nine homolog 1 (EC 1.14.11.29) | protein | 197 | 30% helix, 31% strand | Q9GZT9 |
| B | Egl nine homolog 1 (EC 1.14.11.29) | protein | 202 | 30% helix, 31% strand | Q9GZT9 |
| C | Egl nine homolog 1 (EC 1.14.11.29) | protein | 202 | 29% helix, 31% strand | Q9GZT9 |
| D | Egl nine homolog 1 (EC 1.14.11.29) | protein | 200 | 31% helix, 32% strand | Q9GZT9 |
| E | Egl nine homolog 1 (EC 1.14.11.29) | protein | 198 | 29% helix, 31% strand | Q9GZT9 |
| F | Egl nine homolog 1 (EC 1.14.11.29) | protein | 197 | 28% helix, 32% strand | Q9GZT9 |
Ligands and binding sites
- QEE · ~{tert}-butyl 6-[5-oxidanyl-4-(1,2,3-triazol-1-yl) pyrazol-1-yl]pyridine-3-carboxylate · ligand · 6 copies · chains A, D, B, C, E, F
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · chains B, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 907 | 0.80 | 0.82 | 82 | QEE, MN |
| 2 | 925 | 0.79 | 0.81 | 86 | QEE, MN, GOL |
| 3 | 843 | 0.79 | 0.82 | 67 | empty |
| 4 | 915 | 0.79 | 0.81 | 64 | empty |
| 5 | 1075 | 0.78 | 0.80 | 85 | QEE, MN |
Interfaces
12 interfaces between chains.
- E–F · 843 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 826 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 822 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 451 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 451 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
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 6ZBN · PDBe 6ZBN · UniProt Q9GZT9
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