MolNFT v1 · #164254 · protein
Kemp eliminase HG3.17 mutant Q50K, E47N, N300D complexed with transition state analog 6-nitrobenzotriazole
6SS3 · Kemp eliminase HG3.17 Q50K, E47N, N300D: “Kemp eliminase HG3.17 mutant Q50K, E47N, N300D complexed with transition state analog 6-nitrobenzotriazole”. X-ray diffraction, 2 ligands (6NT, SO4), 2 pockets (best druggability 0.81).…
- PDB
- 6SS3
- Type
- protein
- Length
- 604 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kemp eliminase HG3.17 Q50K, E47N, N300D
- Ligands
- 6NT, SO4
- Pockets
- 2 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kemp eliminase HG3.17 Q50K, E47N, N300D | protein | 305 | 43% helix, 19% strand | — |
| B | Kemp eliminase HG3.17 Q50K, E47N, N300D | protein | 299 | 44% helix, 20% strand | — |
Ligands and binding sites
- 6NT · 6-nitrobenzotriazole · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 663 | 0.81 | 0.85 | 76 | GOL, 6NT |
| 2 | 238 | 0.67 | 0.84 | 40 | 6NT |
Interfaces
1 interface between chains.
- A–B · 883 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6SS3 · Kemp Eliminase HG3.17 mutant Q50K, E47N, N300D Complexed with Transition State Analog… · 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
- Elsewhere: RCSB PDB 6SS3 · PDBe 6SS3
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