Research workbench
Structure of the complex of L-benzylsuccinate with wheat serine carboxypeptidase II at 2.0 ångströms resolution
Analyse Structure of the complex of L-benzylsuccinate with wheat serine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WHS
- Type
- protein
- Length
- 408 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine carboxypeptidase II
- EC
- 3.4.16.1
- UniProt
- P08819
- Ligands
- NAG, FUC
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine carboxypeptidase II (EC 3.4.16.1) | protein | 255 | 38% helix, 22% strand | P08819 |
| B | Serine carboxypeptidase II (EC 3.4.16.1) | protein | 153 | 37% helix, 22% strand | P08819 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · chains A, B
- ACY · Acetic acid · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 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 | 482 | 0.66 | 0.78 | 52 | ACY |
| 2 | 99 | 0.36 | 0.74 | 21 | empty |
| 3 | 88 | 0.35 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 4301 Ų buried · 58 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1WHS · Structure of the complex of L-benzylsuccinate with wheat serine carboxypeptidase II at… · the same entry in another collection · chain A against A, TM-score 1.00
- P08819 · AlphaFold monomer V2.0 prediction for serine carboxypeptidase 2 (P08819) · 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 P08819
- Elsewhere: RCSB PDB 1WHS · PDBe 1WHS · UniProt P08819
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