MolNFT v1 · #169993 · protein
Crystal structure of haloalkane dehalogenase variant DHAA115 domain- swapped dimer type-2
6XT8 · Haloalkane dehalogenase variant DHAA115 domain-swapped…: “Crystal structure of haloalkane dehalogenase variant DHAA115 domain- swapped dimer type-2”. X-ray diffraction, 1 ligand (CL), 5 pockets (best druggability 0.75). MolNFT v1…
- PDB
- 6XT8
- Type
- protein
- Length
- 1,164 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Haloalkane dehalogenase variant DHAA115 domain-swapped dimer type-2
- EC
- 3.8.1.5
- Ligands
- CL
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Haloalkane dehalogenase variant DHAA115 domain-swapped dimer type-2 (EC 3.8.1.5) | protein | 290 | 46% helix, 19% strand | — |
| B, D | Haloalkane dehalogenase variant DHAA115 domain-swapped dimer type-2 (EC 3.8.1.5) | protein | 292 | 45% helix, 19% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 7 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, C, D
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 824 | 0.75 | 0.79 | 55 | GOL |
| 2 | 820 | 0.75 | 0.79 | 59 | GOL |
| 3 | 96 | 0.67 | 0.91 | 33 | CL |
| 4 | 175 | 0.47 | 0.76 | 20 | GOL |
| 5 | 62 | 0.28 | 0.73 | 11 | empty |
Interfaces
4 interfaces between chains.
- C–D · 7315 Ų buried · 103 hydrogen bonds · protein-protein
- A–B · 7186 Ų buried · 106 hydrogen bonds · protein-protein
- A–C · 310 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 241 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6XT8 · Crystal structure of haloalkane dehalogenase variant DhaA115 domain-swapped dimer type-2 · the same entry in another collection · chain C against C, 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 6XT8 · PDBe 6XT8
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