1D6P

HUMAN LYSOZYME L63 MUTANT LABELLED WITH 2',3'-EPOXYPROPYL N,N'-DIACETYLCHITOBIOSE

• PDB DOI: https://doi.org/10.2210/pdb1D6P/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Mutation(s): Yes 


• Deposited: 1999-10-15 Released: 2000-01-21 
• Deposition Author(s): Muraki, M., Harata, K., Sugita, N., Sato, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 0.216 
• R-Value Work: 0.181 
• R-Value Observed: 0.181 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15.19 kDa 
• Atom Count: 1,101 
• Modelled Residue Count: 130 
• Deposited Residue Count: 130 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSOZYME	A	130	Homo sapiens	Mutation(s): 1  EC: 3.2.1.17
UniProt & NIH Common Fund Data Resources
Find proteins for P61626 (Homo sapiens) Explore P61626  Go to UniProtKB:  P61626
PHAROS:  P61626 GTEx:  ENSG00000090382

Oligosaccharides

Help

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	B	2		N/A
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 0.216 
• R-Value Work: 0.181 
• R-Value Observed: 0.181 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.2	α = 90
b = 60.78	β = 90
c = 32.73	γ = 90

Software Package:

Software Name	Purpose
MADNESS	data collection
MERGEF	data reduction
X-PLOR	model building
X-PLOR	refinement
MADNESS	data reduction
MERGEF	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-01-21 
Deposition Author(s): Muraki, M., Harata, K., Sugita, N., Sato, K.

Revision History  

• Version 1.0: 2000-01-21
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2018-04-18
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2021-11-03
  Changes: Database references, Structure summary