MolNFT v1 · #67858 · protein
Crystal structure of human glutamate carboxypeptidase II (gcpii) in a complex with dbibzl, a urea-based inhibitor
3IWW · Glutamate carboxypeptidase 2: “Crystal structure of human glutamate carboxypeptidase II (gcpii) in a complex with dbibzl, a urea-based…”. X-ray diffraction, 7 ligands (YZE, NAG, BMA), 7 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 3IWW
- 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
- YZE, NAG, BMA, MAN, ZN, CA, CL
- Pockets
- 7 · best druggability 0.81
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
- YZE · N~2~-{[(1S)-1-carboxybut-3-en-1-yl]carbamoyl}-N~6~-[(4-iodophenyl)carbonyl]-L-lysine · ligand · chains A
- 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
- 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
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 205 | 0.81 | 0.95 | 35 | CL, YZE |
| 2 | 323 | 0.60 | 0.78 | 43 | empty |
| 3 | 63 | 0.57 | 0.89 | 19 | empty |
| 4 | 243 | 0.50 | 0.75 | 36 | empty |
| 5 | 110 | 0.46 | 0.79 | 26 | empty |
Modifications
Observed in the structure: 7 glycan (N-glycosylation).
Compared structures
- 3IWW · Crystal structure of human glutamate carboxypeptidase II (GCPII) in a complex with… · 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 3IWW · PDBe 3IWW · UniProt Q04609
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