6RNC
Liquid Application Method for time-resolved Analyses (LAMA) by serial synchrotron crystallography, Lysozyme with GlcNAc3 - 100ms diffusion time.
- PDB DOI: https://doi.org/10.2210/pdb6RNC/pdb
- Classification: HYDROLASE
- Organism(s): Gallus gallus
- Mutation(s): No 
- Deposited: 2019-05-08 Released: 2019-10-02 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.192 
- R-Value Work: 0.167 
- R-Value Observed: 0.168 
wwPDB Validation   3D Report Full Report
This is version 2.1 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 |
Lysozyme C | 129 | Gallus gallus | Mutation(s): 0  EC: 3.2.1.17 | ||
UniProt | |||||
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P00698 | ||||
Sequence AnnotationsExpand | |||||
|
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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | B | 3 | N/A | ||
Glycosylation Resources | |||||
GlyTouCan:  G47362BJ GlyCosmos:  G47362BJ GlyGen:  G47362BJ |
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
CL Query on CL | C [auth A], D [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M | |||
NA Query on NA | E [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_900017 Query on PRD_900017 | B | triacetyl-beta-chitotriose | Oligosaccharide / Inhibitor |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.192 
- R-Value Work: 0.167 
- R-Value Observed: 0.168 
- Space Group: P 43 21 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 78.7 | α = 90 |
b = 78.7 | β = 90 |
c = 37.9 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
CrystFEL | data reduction |
CrystFEL | data scaling |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2019-10-02  Deposition Author(s): Mehrabi, P., Schulz, E.C., Miller, R.J.D.
Revision History (Full details and data files)
- Version 1.0: 2019-10-02
Type: Initial release - Version 1.1: 2019-10-09
Changes: Data collection, Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2024-01-24
Changes: Data collection, Database references, Refinement description, Structure summary