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Crystal structure of human glutamate carboxypeptidase III (GCPIII/NAALADASE II), pseudo-unliganded
Analyse Crystal structure of human glutamate carboxypeptidase III (GCPIII/NAALADASE… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FEC
- Type
- protein
- Length
- 689 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate carboxypeptidase III
- EC
- 3.4.17.21
- UniProt
- Q9Y3Q0
- Ligands
- GLU, NAG, ZN, CA, CL
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate carboxypeptidase III (EC 3.4.17.21) | protein | 689 | 39% helix, 18% strand | Q9Y3Q0 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- MPO · 3[N-morpholino]propane sulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 494 | 0.73 | 0.82 | 48 | GLU, MPO |
| 2 | 239 | 0.52 | 0.76 | 37 | empty |
| 3 | 163 | 0.49 | 0.77 | 18 | empty |
| 4 | 138 | 0.46 | 0.77 | 25 | empty |
Modifications
Observed in the structure: 4 glycan, 1 covalent (N-glycosylation, additive adduct).
Compared structures
- 3FEC · Crystal structure of human Glutamate Carboxypeptidase III (GCPIII/NAALADase II)… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y3Q0 · AlphaFold monomer V2.0 prediction for N-acetylated-alpha-linked acidic dipeptidase 2… · 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 Q9Y3Q0
- Elsewhere: RCSB PDB 3FEC · PDBe 3FEC · UniProt Q9Y3Q0
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