1X3Z
Structure of a peptide:N-glycanase-Rad23 complex
- PDB DOI: https://doi.org/10.2210/pdb1X3Z/pdb
- Classification: HYDROLASE/HYDROLASE INHIBITOR
- Organism(s): Saccharomyces cerevisiae
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2005-05-11 Released: 2005-06-14
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.270
- R-Value Work: 0.236
- R-Value Observed: 0.237
wwPDB Validation 3D Report Full Report
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 |
| peptide: N-glycanase | 335 | Saccharomyces cerevisiae | Mutation(s): 0 EC: 3.5.1.52 |  | |
UniProt | |||||
Find proteins for Q02890 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02890 Go to UniProtKB: Q02890 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q02890 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| UV excision repair protein RAD23 | 72 | Saccharomyces cerevisiae | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for P32628 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32628 Go to UniProtKB: P32628 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P32628 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| peptide PHQ-Val-Ala-Asp-CF0 | C [auth I] | 5 | N/A | Mutation(s): 0 |  |
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ZN Query on ZN | F [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
Biologically Interesting Molecules (External Reference) 2 Unique
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_000338 Query on PRD_000338 | C [auth I] | N-[(benzyloxy)carbonyl]-L-valyl-N-[(1S)-1-(carboxymethyl)-3-fluoro-2-oxopropyl]-L-alaninamide | Peptide-like / Inhibitor |  | |
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_900003 Query on PRD_900003 | D [auth C], E [auth D] | sucrose | Oligosaccharide / Nutrient |  | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.270
- R-Value Work: 0.236
- R-Value Observed: 0.237
- Space Group: P 31 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 128.801 | α = 90 |
| b = 128.801 | β = 90 |
| c = 128.376 | γ = 120 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
| CNS | phasing |
Entry History
Deposition Data
- Released Date: 2005-06-14 Deposition Author(s): Lee, J.-H., Choi, J.M., Lee, C., Yi, K.J., Cho, Y.
Revision History (Full details and data files)
- Version 1.0: 2005-06-14
Type: Initial release - Version 1.1: 2008-04-30
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance - Version 1.3: 2012-12-12
Changes: Other - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
