5XSW

Crystal structure of an archaeal chitinase in the substrate-complex form (P63)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structures of an archaeal chitinase ChiD and its ligand complexes.

Nishitani, Y.Horiuchi, A.Aslam, M.Kanai, T.Atomi, H.Miki, K.

(2018) Glycobiology 28: 418-426


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chitinase
A, B
486Thermococcus chitonophagusMutation(s): 0 
Gene Names: chiD
EC: 3.2.1.14
Find proteins for A0A161KIT4 (Thermococcus chitonophagus)
Go to UniProtKB:  A0A161KIT4
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NDG
Query on NDG

Download SDF File 
Download CCD File 
A, B
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.167 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 182.253α = 90.00
b = 182.253β = 90.00
c = 110.791γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
RESOLVEphasing
Cootmodel building
HKL-2000data processing
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
CRESTJapan--

Revision History 

  • Version 1.0: 2018-05-02
    Type: Initial release
  • Version 1.1: 2018-06-13
    Type: Data collection, Database references