Research workbench
Crystal structure of haloalkane dehalogenase linb 140A+143L+177W+211L mutant (LINB86) from sphingobium japonicum UT26
Analyse Crystal structure of haloalkane dehalogenase linb 140A+143L+177W+211L mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WDR
- Type
- protein
- Length
- 585 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Haloalkane dehalogenase
- EC
- 3.8.1.5
- UniProt
- D4Z2G1
- Ligands
- CA, CL
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Haloalkane dehalogenase (EC 3.8.1.5) | protein | 293 | 42% helix, 20% strand | D4Z2G1 |
| B | Haloalkane dehalogenase (EC 3.8.1.5) | protein | 292 | 42% helix, 20% strand | D4Z2G1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.76 | 0.97 | 19 | CL |
| 2 | 621 | 0.64 | 0.75 | 55 | empty |
| 3 | 53 | 0.37 | 0.80 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 277 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4WDR · Crystal structure of haloalkane dehalogenase LinB 140A+143L+177W+211L mutant (LinB86)… · the same entry in another collection · chain A against A, TM-score 1.00
- D4Z2G1 · AlphaFold monomer V2.0 prediction for haloalkane dehalogenase (D4Z2G1) · a predicted model of the same protein · 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
- Every structure of UniProt D4Z2G1
- Elsewhere: RCSB PDB 4WDR · PDBe 4WDR · UniProt D4Z2G1
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