MolNFT v1 · #116062 · protein
X-ray structure of human glutamate carboxypeptidase II (gcpii) in complex with a hydroxamate inhibitor JHU241
5D29 · Glutamate carboxypeptidase 2: “X-ray structure of human glutamate carboxypeptidase II (gcpii) in complex with a hydroxamate inhibitor JHU241”. X-ray diffraction, 6 ligands (5Q1, NAG, BMA), 6 pockets (best druggability 0.78). MolNFT…
- PDB
- 5D29
- Type
- protein
- Length
- 686 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
- 5Q1, NAG, BMA, ZN, CA, CL
- Pockets
- 6 · best druggability 0.78
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 | 686 | 39% helix, 19% strand | Q04609 |
Ligands and binding sites
- 5Q1 · 4-[(2~{S})-2-carboxy-5-(oxidanylamino)-5-oxidanylidene-pentyl]benzoic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies
- ZN · Zinc ion · metal · 2 copies · chains A
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- ACT · Acetate ion · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 639 | 0.78 | 0.83 | 78 | ZN, ACT, 5Q1 |
| 2 | 255 | 0.54 | 0.76 | 44 | empty |
| 3 | 122 | 0.42 | 0.76 | 20 | empty |
| 4 | 70 | 0.34 | 0.76 | 16 | empty |
| 5 | 62 | 0.31 | 0.75 | 13 | empty |
Modifications
Observed in the structure: 7 glycan (N-glycosylation).
Compared structures
- Q04609 · AlphaFold monomer V2.0 prediction for glutamate carboxypeptidase 2 (Q04609) · a predicted model of the same protein · 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 Q04609
- Elsewhere: RCSB PDB 5D29 · PDBe 5D29 · UniProt Q04609
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.