MolNFT v1 · #177469 · protein
Crystal structure of kred F147L/L153Q/Y190P/L199A/M205F/M206F variant and methyl methacrylate complex
7EJI · 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase: “Crystal structure of kred F147L/L153Q/Y190P/L199A/M205F/M206F variant and methyl methacrylate complex”. X-ray diffraction, 4 ligands (NAP, J66, J69), 13 pockets (best druggability…
- PDB
- 7EJI
- Type
- protein
- Length
- 1,007 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, J69, MG
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | protein | 253 | 46% helix, 16% strand | Q6WVP7 |
| B, C | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | protein | 251 | 47% helix, 16% strand | Q6WVP7 |
| D | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | protein | 252 | 47% helix, 15% 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 · 2 copies · chains A, C
- J69 · methyl 2-methylprop-2-enoate · ligand · 2 copies · chains B, D
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, C, D, B
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, D, B, C
- PEG · Di(hydroxyethyl)ether · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 643 | 0.85 | 0.90 | 46 | EDO |
| 2 | 1179 | 0.83 | 0.84 | 120 | NAP, J66, J69 |
| 3 | 571 | 0.78 | 0.84 | 61 | NAP, J66 |
| 4 | 501 | 0.77 | 0.84 | 51 | NAP, J69 |
| 5 | 80 | 0.46 | 0.82 | 12 | BTB |
Interfaces
6 interfaces between chains.
- A–C · 1692 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1686 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1661 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1657 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 327 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7EJI · Crystal structure of KRED F147L/L153Q/Y190P/L199A/M205F/M206F variant and methyl… · the same entry in another collection · chain B against B, 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 7EJI · PDBe 7EJI · UniProt Q6WVP7
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