Research workbench
Structure of drosophila melanogaster carboxypeptidase D isoform 1B short
Analyse Structure of drosophila melanogaster carboxypeptidase D isoform 1B short in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MN8
- Type
- protein
- Length
- 1,539 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LP15968P
- UniProt
- D3DME3
- Ligands
- GEM, NAG, ZN
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LP15968P | protein | 383 | 31% helix, 22% strand | D3DME3 |
| B | LP15968P | protein | 386 | 29% helix, 22% strand | D3DME3 |
| C | LP15968P | protein | 385 | 30% helix, 21% strand | D3DME3 |
| D | LP15968P | protein | 385 | 30% helix, 22% strand | D3DME3 |
Ligands and binding sites
- GEM · (2-guanidinoethylmercapto)succinic acid · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1191 | 0.83 | 0.84 | 105 | empty |
| 2 | 1176 | 0.82 | 0.83 | 108 | empty |
| 3 | 254 | 0.64 | 0.82 | 43 | empty |
| 4 | 67 | 0.55 | 0.88 | 19 | GEM |
| 5 | 73 | 0.54 | 0.87 | 19 | GEM, GOL |
Interfaces
4 interfaces between chains.
- C–D · 1044 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1007 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 222 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 27 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 3MN8 · Structure of Drosophila melanogaster carboxypeptidase D isoform 1B short · 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 D3DME3
- Elsewhere: RCSB PDB 3MN8 · PDBe 3MN8 · UniProt D3DME3
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