Download Mendeleyx-ray snap shots of inhibitor binding process in photo-reactive nitrile hydratase
Nojiri, M., Kawano, Y., Hashimoto, K., Kamiya, N.To be published.
2CZ6 | pdb_00002cz6
Complex of Inactive Fe-type NHase with Cyclohexyl isocyanide
- PDB DOI: https://doi.org/10.2210/pdb2CZ6/pdb
- Classification: LYASE
- Organism(s): Rhodococcus erythropolis
- Mutation(s): Yes
- Deposited: 2005-07-11 Released: 2006-01-11
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.50 Å
- R-Value Free: 0.157 (Depositor), 0.150 (DCC)
- R-Value Work: 0.153 (Depositor), 0.146 (DCC)
- R-Value Observed: 0.153 (Depositor)
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 |
| Nitrile hydratase subunit alpha | 206 | Rhodococcus erythropolis | Mutation(s): 2 EC: 4.2.1.84 |  | |
UniProt | |||||
Find proteins for P13448 (Rhodococcus erythropolis) Explore P13448 Go to UniProtKB: P13448 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P13448 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Nitrile hydratase subunit beta | 212 | Rhodococcus erythropolis | Mutation(s): 0 EC: 4.2.1.84 |  | |
UniProt | |||||
Find proteins for P13449 (Rhodococcus erythropolis) Explore P13449 Go to UniProtKB: P13449 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P13449 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CYI Query on CYI | I [auth B] | CYCLOHEXYL ISOCYANIDE C7 H11 N XYZMOVWWVXBHDP-UHFFFAOYSA-N |  | ||
| FE Query on FE | C [auth A] | FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N |  | ||
| NO Query on NO | G [auth A] | NITRIC OXIDE N O ODUCDPQEXGNKDN-UHFFFAOYSA-N |  | ||
| MG Query on MG | D [auth A], E [auth A], F [auth A], H [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
| Modified Residues 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| CSD Query on CSD | A | L-PEPTIDE LINKING | C3 H7 N O4 S |  | CYS |
| CSO Query on CSO | A | L-PEPTIDE LINKING | C3 H7 N O3 S |  | CYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.50 Å
- R-Value Free: 0.157 (Depositor), 0.150 (DCC)
- R-Value Work: 0.153 (Depositor), 0.146 (DCC)
- R-Value Observed: 0.153 (Depositor)
Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 114.917 | α = 90 |
| b = 60.477 | β = 124.92 |
| c = 81.796 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CNS | refinement |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
| CNS | phasing |
Entry History
Deposition Data
- Released Date: 2006-01-11 Deposition Author(s): Nojiri, M., Kawano, Y., Hashimoto, K., Kamiya, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Revision History (Full details and data files)
- Version 1.0: 2006-01-11
Type: Initial release - Version 1.1: 2008-04-30
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 1.3: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary
