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A high resolution crystal structure of human glutamate carboxypeptidase II (gcpii) in a complex with dcfbd, a urea-based inhibitor
Analyse A high resolution crystal structure of human glutamate carboxypeptidase II… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D7D
- Type
- protein
- Length
- 694 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate carboxypeptidase 2
- EC
- 3.4.17.21
- UniProt
- Q04609
- Ligands
- FBD, NAG, BMA, MAN, ZN, CA, CL
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 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 |
Ligands and binding sites
- FBD · N-({(1R)-1-carboxy-2-[(4-fluorobenzyl)sulfanyl]ethyl}carbamoyl)-L-glutamic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A
- MAN · alpha-D-mannopyranose · sugar
- ZN · Zinc ion · metal · 2 copies · chains A
- 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 491 | 0.76 | 0.84 | 66 | FBD |
| 2 | 122 | 0.56 | 0.83 | 23 | empty |
| 3 | 259 | 0.53 | 0.76 | 39 | empty |
| 4 | 132 | 0.49 | 0.79 | 29 | empty |
| 5 | 82 | 0.31 | 0.73 | 21 | empty |
Modifications
Observed in the structure: 7 glycan (N-glycosylation).
Compared structures
- 3D7D · A high resolution crystal structure of human glutamate carboxypeptidase II (GCPII) in a… · 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 3D7D · PDBe 3D7D · UniProt Q04609
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