Research workbench
Crystal structure of haloalkane dehalogenase variant DHAA115 domain- swapped dimer type-1
Analyse Crystal structure of haloalkane dehalogenase variant DHAA115 domain- swapped… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TY7
- Type
- protein
- Length
- 587 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Haloalkane dehalogenase variant DHAA115 domain-swapped dimer type-1
- EC
- 3.8.1.5
- Ligands
- NO3
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Haloalkane dehalogenase variant DHAA115 domain-swapped dimer type-1 (EC 3.8.1.5) | protein | 290 | 44% helix, 20% strand | — |
| B | Haloalkane dehalogenase variant DHAA115 domain-swapped dimer type-1 (EC 3.8.1.5) | protein | 297 | 44% helix, 19% strand | — |
Ligands and binding sites
- NO3 · Nitrate ion · ion · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, B
- GOL · Glycerol · additive · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.79 | 0.98 | 20 | NO3 |
| 2 | 669 | 0.75 | 0.80 | 64 | PG4 |
| 3 | 154 | 0.65 | 0.86 | 36 | MES |
| 4 | 64 | 0.43 | 0.82 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 6996 Ų buried · 77 hydrogen bonds · protein-protein
Compared structures
- 6TY7 · Crystal structure of haloalkane dehalogenase variant DhaA115 domain-swapped dimer type-1 · 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 6TY7 · PDBe 6TY7
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