3WD3

Serratia marcescens Chitinase B complexed with azide inhibitor

Structural Biology Knowledgebase: 3WD3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.198
  • R-Value Work: 0.169

Literature

Macromolecules
Sequence Display for 3WD3

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 57344.51

Macromolecule Entities
Molecule Chains Length Organism Details
Chitinase B A 503 Serratia marcescens EC#: 3.2.1.14 IUBMB
Gene Name(s): chiB
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
A1L
Query on A1L

A [2-[[(2S)-1-[bis(phenylmethyl)amino]-5-[[N- (methylcarbamoyl)carbamimidoyl]amino]-1-oxidanylidene- pentan-2-yl]amino]-2-oxidanylidene-ethyl]- diazonio-azanide
C24 H31 N9 O3
WCLXSHAWFUUDKF-FQEVSTJZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
A1L N/A in BindingDB
IC50: 580 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.198
  • R-Value Work: 0.169
  • Space Group: P 43 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 97.69 α = 90.00
b = 97.69 β = 90.00
c = 197.43 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-06-06
  • Released Date: 2013-09-18
  • Deposition author(s): Hirose, T., Maita, N., Gouda, H., Koseki, J., Yamamoto, T., Sugawara, A., Nakano, H., Hirono, S., Shiomi, K., Watanabe, T., Taniguchi, H., Sharpless, K.B., Omura, S., Sunazuka, T.

Revision History

  • 2013-11-06
    Type: Citation | Details: Citation update