Download MendeleySubstrate recognition by the leucine aminopeptidase from Vibrio proteolyticus
Kumar, A., Narayanan, B., Kim, J.-J., Bennett, B.To be published.
2NYQ
Structure of Vibrio proteolyticus aminopeptidase with a bound Trp fragment of dLWCF
- PDB DOI: https://doi.org/10.2210/pdb2NYQ/pdb
- Classification: HYDROLASE
- Organism(s): Vibrio proteolyticus, synthetic construct
- Mutation(s): No
- Deposited: 2006-11-21 Released: 2007-10-30
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.256
- R-Value Work: 0.191
- R-Value Observed: 0.191
wwPDB Validation 3D Report Full Report
This is version 1.3 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Aminopeptidase | 299 | Vibrio proteolyticus | Mutation(s): 0 EC: 3.4.11.10 |  | |
UniProt | |||||
Find proteins for Q01693 (Vibrio proteolyticus) Explore Q01693 Go to UniProtKB: Q01693 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q01693 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Tetrapeptide | 4 | synthetic construct | Mutation(s): 0 |  | |
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ZN Query on ZN | C [auth A], D [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.256
- R-Value Work: 0.191
- R-Value Observed: 0.191
- Space Group: P 61 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 107.8 | α = 90 |
| b = 107.8 | β = 90 |
| c = 99.6 | γ = 120 |
| Software Name | Purpose |
|---|---|
| HKL-3000 | data collection |
| AMoRE | phasing |
| CNS | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
Entry History
Deposition Data
- Released Date: 2007-10-30 Deposition Author(s): Bennett, B., Kumar, A., Narayanan, B., Kim, J.-J.
Revision History (Full details and data files)
- Version 1.0: 2007-10-30
Type: Initial release - Version 1.1: 2011-07-13
Changes: Derived calculations, Version format compliance - Version 1.2: 2018-01-24
Changes: Database references, Source and taxonomy, Structure summary - Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description
