3WD1

Serratia marcescens Chitinase B complexed with syn-triazole inhibitor

Structural Biology Knowledgebase: 3WD1 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.186

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3WD1

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 57821.83

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

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ST7
Query on ST7

A N,N-dibenzyl-N~5~-[N-(methylcarbamoyl)carbamimidoyl]- N~2~-{[5-({[(E)-(quinolin-4-ylmethylidene)amino]oxy}methyl)- 1H-1,2,3-triazol-1-yl]acetyl}-L-ornithinamide
C37 H41 N11 O4
YASCYEPUKAYRJI-IPZIAFNWSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

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

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO3
Query on PO3

A PHOSPHITE ION
O3 P
AQSJGOWTSHOLKH-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
ST7 N/A in BindingDB
IC50: 22 nM  BindingMOAD
IC50: 22 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.186
  • Space Group: P 43 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 97.77 α = 90.00
b = 97.77 β = 90.00
c = 197.76 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