4OME
X-ray structure of human glutamate carboxypeptidase II in complex with DCCBL, a urea based inhibitor with distal carborane moiety
- PDB DOI: https://doi.org/10.2210/pdb4OME/pdb
- Classification: Hydrolase/hydrolase inhibitor
- Organism(s): Homo sapiens
- Expression System: Drosophila melanogaster
- Mutation(s): No
- Deposited: 2014-01-27 Released: 2015-02-18
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.79 Å
- R-Value Free: 0.184
- R-Value Work: 0.157
- R-Value Observed: 0.159
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 Gene Names: FOLH, FOLH1, GIG27, NAALAD1, PSM, PSMA 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 | |||||
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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 | 2 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT | |||||
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | D | 3 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE | |||||
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| 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 | |
| DGQ Query on DGQ | M [auth A] | (S)-2-(3-((S)-1-carboxy-5-(1,2-dicarba-closo-dodecarboranylamido) pentyl)ureido)pentanedioic acid C15 H31 B10 N3 O8 NYWNLUFFIRQESZ-YUMQZZPRSA-N |  | ||
| NAG Query on NAG | F [auth A], G [auth A], H [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| ZN Query on ZN | I [auth A], J [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| CA Query on CA | K [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
| CL Query on CL | L [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.79 Å
- R-Value Free: 0.184
- R-Value Work: 0.157
- R-Value Observed: 0.159
- Space Group: I 2 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 101.316 | α = 90 |
| b = 130.564 | β = 90 |
| c = 158.073 | γ = 90 |
| Software Name | Purpose |
|---|---|
| MAR345dtb | data collection |
| REFMAC | refinement |
| XDS | data reduction |
| XDS | data scaling |
| REFMAC | phasing |
Entry History
Deposition Data
- Released Date: 2015-02-18 Deposition Author(s): Barinka, C., Ptacek, J., Novakova, Z., Byun, Y.
Revision History (Full details and data files)
- Version 1.0: 2015-02-18
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
