1KFV

Crystal Structure of Lactococcus lactis Formamido-pyrimidine DNA Glycosylase (alias Fpg or MutM) Non Covalently Bound to an AP Site Containing DNA.

Structural Biology Knowledgebase: 1KFV SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.285
  • R-Value Work: 0.251

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1KFV

Classification: HYDROLASE / DNA

Total Structure Weight: 78343.22


Macromolecule Entities
Molecule Chains Length Organism Details
Formamido-pyrimidine DNA glycosylase A, B 271 Lactococcus lactis EC#: 3.2.2.23 IUBMB
Mutation: P1G, M32M, M75M, M96M, ΔD139, M231M
Gene Name(s): mutM fpg
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*CP*TP*CP*TP*TP*TP*(PDI)P*TP*TP*TP*CP*TP*C)-3' D, G 13 synthetic contains a 1,3 propanediol site (PDI)
5'-D(*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*AP*G)-3' E, H 13 synthetic

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

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

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
PDI
Query on PDI
D, G NON-POLYMER C3 H9 O5 P --
MSE
Query on MSE
A, B L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.285
  • R-Value Work: 0.251
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 69.88 α = 90.00
b = 62.03 β = 104.70
c = 80.97 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-11-23
  • Released Date: 2002-06-14
  • Deposition author(s): Serre, L., Pereira de Jesus, K., Boiteux, S., Zelwer, C., Castaing, B.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update