MolNFT v1 · #118388 · protein
Structure of inactive gcpii mutant in complex with beta-citryl glutamate
5F09 · Glutamate carboxypeptidase 2: “Structure of inactive gcpii mutant in complex with beta-citryl glutamate”. X-ray diffraction, 7 ligands (BC8, NAG, BMA), 7 pockets (best druggability 0.77). MolNFT v1 #118388 on GenesisL1: 3D…
- PDB
- 5F09
- Type
- protein
- Length
- 696 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
- BC8, NAG, BMA, MAN, ZN, CA, CL
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate carboxypeptidase 2 (EC 3.4.17.21) | protein | 696 | 38% helix, 19% strand | Q04609 |
Ligands and binding sites
- BC8 · beta-citryl-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
- PGE · Triethylene glycol · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 652 | 0.77 | 0.83 | 76 | BC8 |
| 2 | 342 | 0.56 | 0.75 | 50 | empty |
| 3 | 91 | 0.38 | 0.76 | 22 | empty |
| 4 | 69 | 0.38 | 0.78 | 15 | empty |
| 5 | 100 | 0.37 | 0.75 | 23 | empty |
Modifications
Observed in the structure: 7 glycan (N-glycosylation).
Compared structures
- 5F09 · Structure of inactive GCPII mutant in complex with beta-citryl glutamate · 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 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 5F09 · PDBe 5F09 · UniProt Q04609
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