2JBJ
membrane-bound glutamate carboxypeptidase II (GCPII) in complex with 2-PMPA (2-phosphonoMethyl-pentanedioic acid)
- PDB DOI: https://doi.org/10.2210/pdb2JBJ/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Drosophila melanogaster
- Mutation(s): No 
- Deposited: 2006-12-07 Released: 2006-12-18 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.19 Å
- R-Value Free: 0.238 
- R-Value Work: 0.192 
- R-Value Observed: 0.193 
This is version 2.0 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 2 | 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 | |
G88 Query on G88 | M [auth A] | (2S)-2-(PHOSPHONOMETHYL)PENTANEDIOIC ACID C6 H11 O7 P ISEYJGQFXSTPMQ-SCSAIBSYSA-N | |||
NAG Query on NAG | J [auth A], K [auth A], L [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
ZN Query on ZN | F [auth A], G [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
CA Query on CA | H [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N | |||
CL Query on CL | I [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
Binding Affinity Annotations  | |||
---|---|---|---|
ID | Source | Binding Affinity | |
G88 | BindingDB:  2JBJ | Ki: min: 0.1, max: 31 (nM) from 8 assay(s) | |
Kd: min: 0.4, max: 0.5 (nM) from 2 assay(s) | |||
IC50: min: 0.1, max: 300 (nM) from 7 assay(s) | |||
EC50: 0.62 (nM) from 1 assay(s) | |||
Binding MOAD:  2JBJ | Ki: 0.2 (nM) from 1 assay(s) | ||
PDBBind:  2JBJ | Ki: 0.2 (nM) from 1 assay(s) |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.19 Å
- R-Value Free: 0.238 
- R-Value Work: 0.192 
- R-Value Observed: 0.193 
- Space Group: I 2 2 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 100.755 | α = 90 |
b = 130.982 | β = 90 |
c = 159.611 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
HKL | data reduction |
SCALEPACK | data scaling |
Entry History 
Deposition Data
- Released Date: 2006-12-18  Deposition Author(s): Mesters, J.R., Henning, K., Hilgenfeld, R.
Revision History (Full details and data files)
- Version 1.0: 2006-12-18
Type: Initial release - Version 1.1: 2011-05-08
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary