1AT5 | pdb_00001at5

HEN EGG WHITE LYSOZYME WITH A SUCCINIMIDE RESIDUE

• PDB DOI: https://doi.org/10.2210/pdb1AT5/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Mutation(s): Yes 


• Deposited: 1997-08-18 Released: 1998-02-25 
• Deposition Author(s): Noguchi, S., Miyawaki, K., Satow, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.233 (Depositor) 
• R-Value Work: 
  0.182 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Succinimide and isoaspartate residues in the crystal structures of hen egg-white lysozyme complexed with tri-N-acetylchitotriose.

Noguchi, S., Miyawaki, K., Satow, Y.

(1998) J Mol Biology 278: 231-238

• PubMed: 9571046 
• DOI: https://doi.org/10.1006/jmbi.1998.1674
• Primary Citation Related Structures: 
  1AT5, 1AT6


• PubMed Abstract: 
  

  The isomerization of Asp101 to isoaspartate autocatalytically proceeds via a succinimide intermediate in hen egg-white lysozyme at a mildly acidic condition. The crystal structures of succinimide and isoaspartate forms of the lysozyme proteins, each complexed with a tri-N-acetylchitotriose ligand, have been determined at 1.8 A resolution, and distinctively elucidate coplanar cyclic aminosuccinyl and beta-linked isoaspartyl residues. Compared with the liganded native protein with normal Asp101, succinimide 101 protrudes toward the ligand, and isoaspartate 101 extends away from the ligand. The formations of these residues caused the loss of three hydrogen-bonds between the ligand and the side-chains of Asp101 and Asn103 along with 0.5 A displacement of the ligand location.

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Organizational Affiliation: 
• Graduate School of Pharmaceutical Sciences, University of Tokyo Hongo 7-3-1, Bunkyo-ku, Tokyo, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 15 kDa 
• Atom Count: 1,142 
• Modeled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSOZYME	A	129	Gallus gallus	Mutation(s): 1  EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SNN	A	L-PEPTIDE LINKING	C4 H6 N2 O2		ASN

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900017	B	triacetyl-beta-chitotriose	Oligosaccharide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.233 (Depositor) 
• R-Value Work:  0.182 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.61	α = 90
b = 78.61	β = 90
c = 38.78	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-02-25 
Deposition Author(s): Noguchi, S., Miyawaki, K., Satow, Y.

Revision History  

• Version 1.0: 1998-02-25
  Type: Initial release
  
• Version 1.1: 2008-03-05
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-08-02
  Changes: Database references, Refinement description, Structure summary
• Version 3.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 4.0: 2024-02-07
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
• Version 4.1: 2024-11-20
  Changes: Structure summary