Research workbench
Crystal structure of kred mutant-F147L/L153Q/Y190P/L199A/M205F/M206F and 2-hydroxyisoindoline-1,3-dione complex
Analyse Crystal structure of kred mutant-F147L/L153Q/Y190P/L199A/M205F/M206F and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EJH
- Type
- protein
- Length
- 1,006 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase
- UniProt
- Q6WVP7
- Ligands
- NAP, J66, MG
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | protein | 253 | 47% helix, 16% strand | Q6WVP7 |
| B, C, D | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | protein | 251 | 46% helix, 16% strand | Q6WVP7 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- J66 · 2-oxidanylisoindole-1,3-dione · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 641 | 0.85 | 0.90 | 49 | empty |
| 2 | 611 | 0.78 | 0.84 | 66 | NAP, J66 |
| 3 | 573 | 0.78 | 0.84 | 62 | NAP, J66 |
| 4 | 551 | 0.78 | 0.84 | 57 | NAP, J66 |
| 5 | 517 | 0.77 | 0.84 | 52 | NAP, J66 |
Interfaces
6 interfaces between chains.
- A–C · 1693 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1690 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1677 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1604 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 313 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7EJH · Crystal structure of KRED mutant-F147L/L153Q/Y190P/L199A/M205F/M206F and… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q6WVP7
- Elsewhere: RCSB PDB 7EJH · PDBe 7EJH · UniProt Q6WVP7
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