3LMC

Crystal Structure of zinc-dependent peptidase from Methanocorpusculum labreanum (strain Z), Northeast Structural Genomics Consortium Target MuR16


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.997 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Northeast Structural Genomics Consortium Target MuR16

Kuzin, A.Ashok, S.Vorobiev, S.Seetharaman, J.Patel, P.Xiao, R.Ciccosanti, C.Lee, D.Everett, J.K.Nair, R.Acton, T.B.Rost, B.Montelione, G.T.Tong, L.Hunt, J.F.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidase, zinc-dependent
A
210Methanocorpusculum labreanum (strain ATCC 43576 / DSM 4855 / Z)Mutation(s): 0 
Find proteins for A2SQK8 (Methanocorpusculum labreanum (strain ATCC 43576 / DSM 4855 / Z))
Go to UniProtKB:  A2SQK8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.997 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.212 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 89.627α = 90.00
b = 60.889β = 101.19
c = 47.859γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SnBphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2010-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-11-16
    Type: Atomic model
  • Version 1.3: 2017-11-01
    Type: Refinement description
  • Version 1.4: 2018-01-24
    Type: Database references, Structure summary