MolNFT v1 · #59425 · protein
Structure of an inactive mutant of human glutamate carboxypeptidase II [GCPII(E424A)] in complex with N-acetyl-asp-glu (naag)
3BXM · Glutamate carboxypeptidase 2: “Structure of an inactive mutant of human glutamate carboxypeptidase II [GCPII(E424A)] in complex with…”. X-ray diffraction, 7 ligands (ACE, NAG, BMA), 6 pockets (best druggability 0.56). MolNFT v1…
- PDB
- 3BXM
- Type
- protein
- Length
- 696 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate carboxypeptidase 2; N-acetyl-aspartyl-glutamate (naag)
- EC
- 3.4.17.21
- UniProt
- Q04609
- Ligands
- ACE, NAG, BMA, MAN, ZN, CA, CL
- Pockets
- 6 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate carboxypeptidase 2 (EC 3.4.17.21) | protein | 694 | 39% helix, 19% strand | Q04609 |
| I | N-acetyl-aspartyl-glutamate (naag) | protein | 2 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A, I
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- ZN · Zinc ion · metal · 2 copies · chains A, I
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.56 | 0.82 | 21 | empty |
| 2 | 271 | 0.56 | 0.77 | 40 | empty |
| 3 | 260 | 0.54 | 0.76 | 44 | empty |
| 4 | 167 | 0.53 | 0.79 | 39 | empty |
| 5 | 57 | 0.36 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–I · 315 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 glycan, 1 covalent (N-glycosylation, covalent ligand).
Compared structures
- 3BXM · Structure of an inactive mutant of human glutamate carboxypeptidase II [GCPII(E424A)] in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q04609 · AlphaFold monomer V2.0 prediction for glutamate carboxypeptidase 2 (Q04609) · 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 Q04609
- Elsewhere: RCSB PDB 3BXM · PDBe 3BXM · UniProt Q04609
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