MolNFT v1 · #26196 · protein
Structure of the complex of L-benzylsuccinate with wheat serine carboxypeptidase II at 2.0 ångströms resolution
1WHT: “Structure of the complex of L-benzylsuccinate with wheat serine carboxypeptidase II at 2.0 ångströms…”. X-ray diffraction, 4 ligands (BZS, NAG, FUC), 3 pockets (best druggability 0.66). MolNFT v1 #26196 on GenesisL1: 3D structure…
- PDB
- 1WHT
- Type
- protein
- Length
- 409 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
- BZS, NAG, FUC, NDG
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine carboxypeptidase II (EC 3.4.16.1) | protein | 256 | 39% helix, 21% strand | P08819 |
| B | Serine carboxypeptidase II (EC 3.4.16.1) | protein | 153 | 37% helix, 22% strand | P08819 |
Ligands and binding sites
- BZS · L-benzylsuccinic acid · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · chains A, B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains B
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 | 476 | 0.66 | 0.78 | 49 | BZS |
| 2 | 100 | 0.38 | 0.75 | 20 | empty |
| 3 | 105 | 0.37 | 0.74 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 4318 Ų buried · 59 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 1WHT · 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 1WHT · PDBe 1WHT · UniProt P08819
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