2CIJ
membrane-bound glutamate carboxypeptidase II (GCPII) with bound methionine
- PDB DOI: https://doi.org/10.2210/pdb2CIJ/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Drosophila melanogaster
- Mutation(s): No
- Deposited: 2006-03-21 Released: 2007-03-27
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.219
- R-Value Work: 0.172
- R-Value Observed: 0.174
This is version 2.1 of the entry. See complete history.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| GLUTAMATE CARBOXYPEPTIDASE II | 707 | Homo sapiens | Mutation(s): 0 EC: 3.4.17.21 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q04609 (Homo sapiens) Explore Q04609 Go to UniProtKB: Q04609 | |||||
PHAROS: Q04609 GTEx: ENSG00000086205 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q04609 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Oligosaccharides
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | B, C, D | 2 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT | |||||
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | E | 4 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD | |||||
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | K [auth A], L [auth A], M [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| MET Query on MET | F [auth A] | METHIONINE C5 H11 N O2 S FFEARJCKVFRZRR-BYPYZUCNSA-N |  | ||
| ZN Query on ZN | G [auth A], H [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| CA Query on CA | I [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
| CL Query on CL | J [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.219
- R-Value Work: 0.172
- R-Value Observed: 0.174
- Space Group: I 2 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 102.692 | α = 90 |
| b = 130.777 | β = 90 |
| c = 160.303 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
Entry History
Deposition Data
- Released Date: 2007-03-27 Deposition Author(s): Barinka, C., Plechanovova, A., Rulisek, L., Mlcochova, P., Majer, P., Slusher, B.S., Hilgenfeld, R., Mesters, J.R., Konvalinka, J.
Revision History (Full details and data files)
- Version 1.0: 2007-03-27
Type: Initial release - Version 1.1: 2014-06-11
Changes: Database references, Derived calculations, Other, Structure summary, Version format compliance - Version 1.2: 2019-07-24
Changes: Data collection, Derived calculations - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary - Version 2.1: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
