5NJC

E. coli Microcin-processing metalloprotease TldD/E (TldD E263A mutant) with hexapeptide bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.183
  • R-Value Work: 0.145

Literature

Macromolecules
Sequence Display for 5NJC

Classification: HYDROLASE

Total Structure Weight: 206024.08

Macromolecule Entities
Molecule Chains Length Organism Details
Metalloprotease TldD A, C 495 Escherichia coli EC#: 3.4 IUBMB
Mutation: E263A, G401D
Details: The TldD protein was expressed with a fourteen residue nickel affinity tag with sequence MGSSHHHHHHSQDP appended to the N-terminus of the full-length amino acid sequence
Gene Name(s): tldD yhdO b3244 JW3213
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Metalloprotease PmbA B, D 450 Escherichia coli EC#: 3.4 IUBMB
Gene Name(s): pmbA tldE b4235 JW4194
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
VAL-LEU-GLU-ASP-ARG-ILE E, F 6 Escherichia coli Details: Peptide adventitiously bound in the active site. From electron density a match was found to residues 49-54 of TldD, but this identification was not independently verified.

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

A, B, C, D 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, C ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, B, C, D 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, B, C, D SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.183
  • R-Value Work: 0.145
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 65.29 α = 90.00
b = 175.44 β = 90.01
c = 84.33 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2017-03-28
  • Released Date: 2017-10-04
  • Deposition author(s): Ghilarov, D., Serebryakova, M., Stevenson, C.E.M., Hearnshaw, S.J., Volkov, D., Maxwell, A., Lawson, D.M., Severinov, K.

Revision History

  • Version 1_0: 2017-10-04

    Type: Initial release

  • Version 1_1: 2017-10-18

    Type: Database references