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The crystal structure of a hydrolase from pseudomonas syringae
Analyse The crystal structure of a hydrolase from pseudomonas syringae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S6J
- Type
- protein
- Length
- 1,292 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrolase, haloacid dehalogenase-like family
- UniProt
- Q88AV7
- Ligands
- CA
- Pockets
- 19 · best druggability 0.64
Structure
x-ray diffraction · 6 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydrolase, haloacid dehalogenase-like family | protein | 216 | 52% helix, 13% strand | Q88AV7 |
| B | Hydrolase, haloacid dehalogenase-like family | protein | 209 | 48% helix, 13% strand | Q88AV7 |
| C | Hydrolase, haloacid dehalogenase-like family | protein | 212 | 48% helix, 13% strand | Q88AV7 |
| D | Hydrolase, haloacid dehalogenase-like family | protein | 216 | 52% helix, 14% strand | Q88AV7 |
| E | Hydrolase, haloacid dehalogenase-like family | protein | 220 | 55% helix, 13% strand | Q88AV7 |
| F | Hydrolase, haloacid dehalogenase-like family | protein | 219 | 53% helix, 13% strand | Q88AV7 |
Ligands and binding sites
- CA · Calcium ion · metal · 9 copies · chains A, B, F, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 270 | 0.64 | 0.81 | 39 | CA |
| 2 | 502 | 0.63 | 0.76 | 55 | empty |
| 3 | 177 | 0.62 | 0.84 | 34 | CA |
| 4 | 168 | 0.61 | 0.84 | 33 | empty |
| 5 | 255 | 0.61 | 0.80 | 44 | CA |
Interfaces
8 interfaces between chains.
- C–D · 954 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 941 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 933 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 199 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 190 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 modified (engineered).
Compared structures
- 3S6J · The crystal structure of a hydrolase from Pseudomonas syringae · 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 Q88AV7
- Elsewhere: RCSB PDB 3S6J · PDBe 3S6J · UniProt Q88AV7
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