MolNFT v1 · #1798 · protein
Complex of the wheat serine carboxypeptidase, cpdw-II, with the microbial peptide aldehyde inhibitor, chymostatin, and arginine at 100 degrees kelvin
1BCS · Serine carboxypeptidase II: “Complex of the wheat serine carboxypeptidase, cpdw-II, with the microbial peptide aldehyde inhibitor…”. X-ray diffraction, 4 ligands (ARG, NAG, FUC), 3 pockets (best druggability 0.69). MolNFT v1 #1798…
- PDB
- 1BCS
- Type
- protein
- Length
- 412 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine carboxypeptidase II; Chymostatin a
- EC
- 3.4.16.6
- UniProt
- P08819
- Ligands
- ARG, NAG, FUC, NDG
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine carboxypeptidase II (EC 3.4.16.6) | protein | 255 | 38% helix, 22% strand | P08819 |
| B | Serine carboxypeptidase II (EC 3.4.16.6) | protein | 153 | 37% helix, 22% strand | P08819 |
| C | Chymostatin a | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- ARG · Arginine · ligand · chains A, B, C
- 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
- GOL · Glycerol · additive · chains A
- ACT · Acetate ion · additive · 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 | 379 | 0.69 | 0.81 | 48 | ARG |
| 2 | 95 | 0.35 | 0.74 | 20 | empty |
| 3 | 78 | 0.33 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 4320 Ų buried · 63 hydrogen bonds · protein-protein
- A–C · 298 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 253 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- 1BCS · Complex of the wheat serine carboxypeptidase, cpdw-II, with the microbial peptide… · 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 1BCS · PDBe 1BCS · UniProt P08819
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