4HP0
Crystal Structure of Hen Egg White Lysozyme in complex with GN3-M
- PDB DOI: https://doi.org/10.2210/pdb4HP0/pdb
- Classification: HYDROLASE/HYDROLASE INHIBITOR
- Organism(s): Gallus gallus
- Mutation(s): No 
- Deposited: 2012-10-23 Released: 2013-01-16 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.19 Å
- R-Value Free: 0.173 
- R-Value Work: 0.164 
- R-Value Observed: 0.165 
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 | |||||
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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 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NOJ Query on NOJ | C [auth A] | 1-DEOXYNOJIRIMYCIN C6 H13 N O4 LXBIFEVIBLOUGU-JGWLITMVSA-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: 1.19 Å
- R-Value Free: 0.173 
- R-Value Work: 0.164 
- R-Value Observed: 0.165 
- Space Group: P 43 21 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 76.817 | α = 90 |
b = 76.817 | β = 90 |
c = 38.081 | γ = 90 |
Software Name | Purpose |
---|---|
HKL-2000 | data collection |
MOLREP | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
Entry History 
Deposition Data
- Released Date: 2013-01-16  Deposition Author(s): Umemoto, N., Numata, T., Ohnuma, T., Fukamizo, T.
Revision History (Full details and data files)
- Version 1.0: 2013-01-16
Type: Initial release - Version 1.1: 2013-03-13
Changes: Other - Version 1.2: 2014-02-12
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary