Research workbench
Crystal structure of altronate hydrolase (fragment 1-84) from shigella flexneri.
Analyse Crystal structure of altronate hydrolase (fragment 1-84) from shigella flexneri. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K3S
- Type
- protein
- Length
- 679 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Altronate hydrolase
- UniProt
- Q83JJ2
- Ligands
- CL
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G | Altronate hydrolase | protein | 85 | 0% helix, 42% strand | Q83JJ2 |
| H | Altronate hydrolase | protein | 84 | 0% helix, 40% strand | Q83JJ2 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains B, D, G, H
- ACT · Acetate ion · additive · 6 copies · chains B, E, C, F, G, H
- MLA · Malonic acid · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 618 | 0.74 | 0.81 | 57 | ACT |
| 2 | 236 | 0.58 | 0.79 | 26 | MLA |
| 3 | 313 | 0.56 | 0.76 | 27 | ACT |
Interfaces
12 interfaces between chains.
- F–G · 639 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 594 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 553 Ų buried · 5 hydrogen bonds · protein-protein
- C–H · 534 Ų buried · 3 hydrogen bonds · protein-protein
- E–G · 382 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3K3S · Crystal structure of altronate hydrolase (fragment 1-84) from Shigella Flexneri. · 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 Q83JJ2
- Elsewhere: RCSB PDB 3K3S · PDBe 3K3S · UniProt Q83JJ2
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