8PN3

Crystal structure of the HC7-Glu200Ala mutant complexed to a tetraglycopeptide.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A family of di-glutamate mucin-degrading enzymes that bridges glycan hydrolases and peptidases

Narimatsu, Y.Bull, C.Taleb, V.Liao, Q.Companon, I.Sanchez-Navarro, D.Durbesson, F.Vincentelli, R.Hansen, L.Corzana, F.Rovira, C.Henrissat, B.Clausen, H.Joshi, H.J.Hurtado-Guerrero, R.

(2024) Nat Catal 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DUF3472 domain-containing protein
A, B
659Bacillus cereusMutation(s): 0 
Gene Names: DN401_14795
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tetraglycopeptide
C, D
15synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A2G (Subject of Investigation/LOI)
Query on A2G

Download Ideal Coordinates CCD File 
J [auth C]
K [auth C]
L [auth C]
M [auth C]
N [auth D]
J [auth C],
K [auth C],
L [auth C],
M [auth C],
N [auth D],
O [auth D],
P [auth D],
Q [auth D]
2-acetamido-2-deoxy-alpha-D-galactopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.703α = 90
b = 91.94β = 90
c = 99.741γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpain--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-06
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Structure summary