Research workbench
Duck carboxypeptidase D domain II in complex with gemsa
Analyse Duck carboxypeptidase D domain II in complex with gemsa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1H8L
- Type
- protein
- Length
- 380 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxypeptidase GP180 residues 503-882
- UniProt
- Q90240
- Ligands
- GEM, NAG, BMA, ZN, SO4
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carboxypeptidase GP180 residues 503-882 | protein | 380 | 30% helix, 25% strand | Q90240 |
Ligands and binding sites
- GEM · (2-guanidinoethylmercapto)succinic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.58 | 0.87 | 21 | GEM |
| 2 | 68 | 0.45 | 0.82 | 19 | empty |
| 3 | 72 | 0.40 | 0.79 | 20 | empty |
| 4 | 75 | 0.33 | 0.75 | 16 | empty |
Modifications
Observed in the structure: 3 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
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 Q90240
- Elsewhere: RCSB PDB 1H8L · PDBe 1H8L · UniProt Q90240
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