4P7A | pdb_00004p7a

Crystal Structure of human MLH1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.254 (Depositor), 0.256 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4P7A

Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 3NA3

Literature

Structure of the human MLH1 N-terminus: implications for predisposition to Lynch syndrome.

Wu, H.Zeng, H.Lam, R.Tempel, W.Kerr, I.D.Min, J.

(2015) Acta Crystallogr F Struct Biol Commun 71: 981-985

  • DOI: https://doi.org/10.1107/S2053230X15010183
  • Primary Citation Related Structures: 
    4P7A

  • PubMed Abstract: 

    Mismatch repair prevents the accumulation of erroneous insertions/deletions and non-Watson-Crick base pairs in the genome. Pathogenic mutations in the MLH1 gene are associated with a predisposition to Lynch and Turcot's syndromes. Although genetic testing for these mutations is available, robust classification of variants requires strong clinical and functional support. Here, the first structure of the N-terminus of human MLH1, determined by X-ray crystallography, is described. The structure shares a high degree of similarity with previously determined prokaryotic MLH1 homologs; however, this structure affords a more accurate platform for the classification of MLH1 variants.


  • Organizational Affiliation
    • Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada.

Macromolecule Content 

  • Total Structure Weight: 39.11 kDa 
  • Atom Count: 2,296 
  • Modeled Residue Count: 303 
  • Deposited Residue Count: 348 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA mismatch repair protein Mlh1348Homo sapiensMutation(s): 0 
Gene Names: MLH1COCA2
UniProt & NIH Common Fund Data Resources
Find proteins for P40692 (Homo sapiens)
Explore P40692 
Go to UniProtKB:  P40692
PHAROS:  P40692
GTEx:  ENSG00000076242 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40692
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP

Query on ADP



Download:Ideal Coordinates CCD File
C [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNX

Query on UNX



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
UNKNOWN ATOM OR ION
X

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.254 (Depositor), 0.256 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.568α = 90
b = 94.568β = 90
c = 85.825γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
BUSTERrefinement
XDSdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2014-11-12
    Changes: Other
  • Version 1.2: 2015-12-16
    Changes: Database references
  • Version 2.0: 2019-07-17
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
  • Version 2.1: 2023-12-27
    Changes: Data collection, Database references, Derived calculations