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.
2D0Q
Complex of Fe-type NHase with Cyclohexyl isocyanide, photo-activated for 1hr at 277K
- PDB DOI: https://doi.org/10.2210/pdb2D0Q/pdb
- Classification: LYASE
- Organism(s): Rhodococcus erythropolis
- Mutation(s): Yes
- Deposited: 2005-08-05 Released: 2006-02-05
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.65 Å
- R-Value Free: 0.165
- R-Value Work: 0.154
- R-Value Observed: 0.154
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): 1 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 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CYI Query on CYI | H [auth A] | CYCLOHEXYL ISOCYANIDE C7 H11 N XYZMOVWWVXBHDP-UHFFFAOYSA-N |  | ||
| FE Query on FE | C [auth A] | FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N |  | ||
| MG Query on MG | D [auth A] E [auth A] F [auth A] G [auth A] I [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| CSD Query on CSD | A | L-PEPTIDE LINKING | C3 H7 N O4 S |  | CYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.65 Å
- R-Value Free: 0.165
- R-Value Work: 0.154
- R-Value Observed: 0.154
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 114.352 | α = 90 |
| b = 60.201 | β = 125.1 |
| c = 81.585 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
| CNS | phasing |
Entry History
Deposition Data
- Released Date: 2006-02-05 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: 2006-02-05
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: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary
