Research workbench
Crystal structure analysis of a dehalogenase with intermediate complex
Analyse Crystal structure analysis of a dehalogenase with intermediate complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NO5
- Type
- protein
- Length
- 451 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- (S)-2-haloacid dehalogenase iva
- EC
- 3.8.1.2
- UniProt
- Q51645
- Ligands
- CNR, SO4, CL
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | (S)-2-haloacid dehalogenase iva (EC 3.8.1.2) | protein | 225 | 50% helix, 13% strand | Q51645 |
| B | (S)-2-haloacid dehalogenase iva (EC 3.8.1.2) | protein | 226 | 52% helix, 13% strand | Q51645 |
Ligands and binding sites
- CNR · (2S)-2-chloropropanoic acid · ligand · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · 13 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 980 | 0.80 | 0.82 | 63 | SO4, CNR |
| 2 | 56 | 0.37 | 0.79 | 12 | SO4 |
| 3 | 53 | 0.29 | 0.75 | 16 | CL |
Interfaces
1 interface between chains.
- A–B · 1438 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 2NO5 · Crystal Structure analysis of a Dehalogenase with intermediate complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q51645 · AlphaFold monomer V2.0 prediction for (S)-2-haloacid dehalogenase 4A (Q51645) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q51645
- Elsewhere: RCSB PDB 2NO5 · PDBe 2NO5 · UniProt Q51645
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