MolNFT v1 · #72379 · protein
Crystal structure of yghz from E. COLI
3N6Q · Yghz aldo-keto reductase: “Crystal structure of yghz from E. COLI”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.84). MolNFT v1 #72379 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3N6Q
- Type
- protein
- Length
- 2,498 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yghz aldo-keto reductase
- UniProt
- Q46851
- Ligands
- MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yghz aldo-keto reductase | protein | 314 | 44% helix, 15% strand | Q46851 |
| B | Yghz aldo-keto reductase | protein | 315 | 42% helix, 15% strand | Q46851 |
| C, F, G | Yghz aldo-keto reductase | protein | 313 | 43% helix, 15% strand | Q46851 |
| D | Yghz aldo-keto reductase | protein | 315 | 43% helix, 15% strand | Q46851 |
| E | Yghz aldo-keto reductase | protein | 309 | 42% helix, 15% strand | Q46851 |
| H | Yghz aldo-keto reductase | protein | 306 | 41% helix, 15% strand | Q46851 |
Ligands and binding sites
- MG · Magnesium ion · metal · 9 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1004 | 0.84 | 0.85 | 134 | empty |
| 2 | 976 | 0.84 | 0.85 | 115 | empty |
| 3 | 428 | 0.63 | 0.77 | 54 | empty |
| 4 | 178 | 0.57 | 0.81 | 30 | empty |
| 5 | 142 | 0.57 | 0.83 | 23 | empty |
Interfaces
12 interfaces between chains.
- F–G · 949 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 945 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 942 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 937 Ų buried · 12 hydrogen bonds · protein-protein
- E–H · 936 Ų buried · 12 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 Q46851
- Elsewhere: RCSB PDB 3N6Q · PDBe 3N6Q · UniProt Q46851
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