Research workbench
X-ray structure of human glutamate carboxypeptidase II (gcpii) in complex with aptamer A9G
Analyse X-ray structure of human glutamate carboxypeptidase II (gcpii) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RTI
- Type
- protein + DNA
- Length
- 736 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate carboxypeptidase 2; Aptamer A9G, RNA (43-mer)
- EC
- 3.4.17.21
- UniProt
- Q04609
- Ligands
- G88, NAG, BMA, MAN, ZN, CA, CL
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate carboxypeptidase 2 (EC 3.4.17.21) | protein | 693 | 39% helix, 19% strand | Q04609 |
| X | Aptamer A9G, RNA (43-mer) | dna | 43 | — | — |
Ligands and binding sites
- G88 · (2S)-2-(phosphonomethyl)pentanedioic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 4 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
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 6 copies · chains A, X
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 759 | 0.87 | 0.91 | 90 | CL, G88 |
| 2 | 285 | 0.78 | 0.91 | 34 | empty |
| 3 | 59 | 0.52 | 0.87 | 12 | empty |
| 4 | 252 | 0.52 | 0.75 | 36 | empty |
| 5 | 94 | 0.43 | 0.79 | 19 | MPD |
Interfaces
1 interface between chains.
- A–X · 1642 Ų buried · 31 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 22 modified, 7 glycan (nucleotide modification, N-glycosylation).
Compared structures
- 6RTI · X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with aptamer A9g · 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 6RTI · PDBe 6RTI · UniProt Q04609
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