Research workbench
Kemp eliminase HG3.17 mutant Q50M, E47N, N300D complexed with transition state analog 6-nitrobenzotriazole
Analyse Kemp eliminase HG3.17 mutant Q50M, E47N, N300D complexed with transition state… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TU6
- Type
- protein
- Length
- 4,795 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kemp eliminase HG3.17 mutant Q50M, E47N, N300D complexed with transition state analog…
- Ligands
- 6NT, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, I, J, K, L, N | Kemp eliminase HG3.17 mutant Q50M, E47N, N300D complexed with transition state analog 6-nitrobenzotriazole | protein | 300 | 43% helix, 20% strand | — |
| B, C, D, E, G, M, P | Kemp eliminase HG3.17 mutant Q50M, E47N, N300D complexed with transition state analog 6-nitrobenzotriazole | protein | 299 | 44% helix, 20% strand | — |
| H, O | Kemp eliminase HG3.17 mutant Q50M, E47N, N300D complexed with transition state analog 6-nitrobenzotriazole | protein | 301 | 44% helix, 20% strand | — |
Ligands and binding sites
- 6NT · 6-nitrobenzotriazole · ligand · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- SO4 · Sulfate ion · ion · 24 copies · chains A, G, B, C, D, L, E, F, H, I, J, M, N, P, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 548 | 0.82 | 0.88 | 67 | 6NT |
| 2 | 611 | 0.81 | 0.86 | 73 | 6NT |
| 3 | 326 | 0.80 | 0.90 | 39 | empty |
| 4 | 347 | 0.79 | 0.89 | 42 | empty |
| 5 | 863 | 0.75 | 0.79 | 100 | empty |
Interfaces
28 interfaces between chains.
- A–G · 878 Ų buried · 19 hydrogen bonds · protein-protein
- E–I · 875 Ų buried · 18 hydrogen bonds · protein-protein
- N–P · 873 Ų buried · 20 hydrogen bonds · protein-protein
- B–H · 865 Ų buried · 17 hydrogen bonds · protein-protein
- D–N · 491 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6TU6 · Kemp Eliminase HG3.17 mutant Q50M, 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 6TU6 · PDBe 6TU6
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