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Crystal structure of a hydrolase, haloacid dehalogenase-like family from brucella suis 1330
Analyse Crystal structure of a hydrolase, haloacid dehalogenase-like family from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NQ4
- Type
- protein
- Length
- 532 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Had superfamily hydrolase
- UniProt
- A0A0H3GA96
- Ligands
- NA, PO4
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Had superfamily hydrolase | protein | 271 | 39% helix, 21% strand | A0A0H3GA96 |
| B | Had superfamily hydrolase | protein | 261 | 41% helix, 20% strand | A0A0H3GA96 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1159 | 0.76 | 0.78 | 122 | EDO, PO4, NA |
| 2 | 313 | 0.67 | 0.82 | 48 | EDO, PO4 |
| 3 | 86 | 0.40 | 0.78 | 20 | empty |
| 4 | 79 | 0.39 | 0.78 | 19 | empty |
| 5 | 73 | 0.36 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 825 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6NQ4 · Crystal structure of a Hydrolase, haloacid dehalogenase-like family from Brucella suis… · 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
- Every structure of UniProt A0A0H3GA96
- Elsewhere: RCSB PDB 6NQ4 · PDBe 6NQ4 · UniProt A0A0H3GA96
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