7XF6 | pdb_00007xf6

Crystal Structure of Human Lysozyme

  • Classification: HYDROLASE
  • Organism(s): Homo sapiens
  • Expression System: Oryza sativa
  • Mutation(s): No 

  • Deposited: 2022-04-01 Released: 2022-04-13 
  • Deposition Author(s): Nam, K.H.
  • Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 
    0.171 (Depositor), 0.171 (DCC) 
  • R-Value Work: 
    0.151 (Depositor), 0.152 (DCC) 
  • R-Value Observed: 
    0.153 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history. 

Literature

Crystal Structure of Human Lysozyme Complexed with N-Acetyl-alpha-d-glucosamine.

Nam, K.H.

(2022) Appl Sci (Basel) 12

Macromolecule Content 

  • Total Structure Weight: 14.78 kDa 
  • Atom Count: 1,296 
  • Modeled Residue Count: 130 
  • Deposited Residue Count: 130 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lysozyme C130Homo sapiensMutation(s): 0 
Gene Names: LYZ, LZM
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61626
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACT
(Subject of Investigation/LOI)

Query on ACT


Download:Ideal Coordinates CCD File
B [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free:  0.171 (Depositor), 0.171 (DCC) 
  • R-Value Work:  0.151 (Depositor), 0.152 (DCC) 
  • R-Value Observed: 0.153 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.035α = 90
b = 56.062β = 90
c = 61.063γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data

  • Released Date: 2022-04-13 
    • Deposition Author(s): Nam, K.H.
Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2017M3A9F6029736
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2021R1I1A1A01050838
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2020M3H1A1075314

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-13
    Type: Initial release
  • Version 1.1: 2022-10-26
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary