Research workbench
Crystal structure of haloalkane dehalogenase HALOTAG7 at the resolution 1.5A, northeast structural genomics consortium (nesg) target OR151
Analyse Crystal structure of haloalkane dehalogenase HALOTAG7 at the resolution 1.5A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KAF
- Type
- protein
- Length
- 595 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Haloalkane dehalogenase
- EC
- 3.8.1.5
- UniProt
- P0A3G3
- Ligands
- NA, SCN
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Haloalkane dehalogenase (EC 3.8.1.5) | protein | 296 | 44% helix, 19% strand | P0A3G3 |
| B | Haloalkane dehalogenase (EC 3.8.1.5) | protein | 299 | 44% helix, 19% strand | P0A3G3 |
Ligands and binding sites
- NA · Sodium ion · metal · 6 copies · chains A, B
- SCN · Thiocyanate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains B
- PEG · Di(hydroxyethyl)ether · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.71 | 0.98 | 20 | SCN |
| 2 | 596 | 0.67 | 0.77 | 65 | NA, PEG |
| 3 | 108 | 0.66 | 0.89 | 24 | SCN |
| 4 | 301 | 0.55 | 0.76 | 47 | NA |
Interfaces
1 interface between chains.
- A–B · 456 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 4KAF · Crystal Structure of Haloalkane dehalogenase HaloTag7 at the resolution 1.5A, Northeast… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A3G3 · AlphaFold monomer V2.0 prediction for haloalkane dehalogenase (P0A3G3) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P0A3G3
- Elsewhere: RCSB PDB 4KAF · PDBe 4KAF · UniProt P0A3G3
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