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Polymerase Domain from Mycobacterium tuberculosis Ligase D in complex with an annealed double-strand DNA break.

X-ray diffraction
2.4Å resolution
PDB entry 4mky coloured by chain, front view.
PDB entry 4mky coloured by chain, side view.
PDB entry 4mky coloured by chain, top view.
Source organism: Mycobacterium tuberculosis
Assembly composition:
hetero hexamer (preferred)
Entry contents: 1 distinct polypeptide molecule
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Multifunctional non-homologous end joining DNA repair protein LigD and DNA
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Multimeric state: hetero hexamer
Accessible surface area: 27239.97 Å2
Buried surface area: 5828.66 Å2
Dissociation area: 458.18 Å2
Dissociation energy (ΔGdiss): 5.46 kcal/mol
Dissociation entropy (TΔSdiss): 6.76 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-117856
Assembly 2
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Assembly Name: Multifunctional non-homologous end joining DNA repair protein LigD and DNA
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Multimeric state: hetero hexamer
Accessible surface area: 26960.17 Å2
Buried surface area: 5854.1 Å2
Dissociation area: 447.69 Å2
Dissociation energy (ΔGdiss): 5.23 kcal/mol
Dissociation entropy (TΔSdiss): 6.73 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-117856

Macromolecules

Multifunctional non-homologous end joining DNA repair protein LigD
Chains: A, B, C, D
Length: 303 amino acids
Theoretical weight: 32.83 KDa
Source organism: Mycobacterium tuberculosis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P9WNV3 (Residues: 1-300; Coverage: 40%)
Gene names: MTCY08D9.01c, MTCY10D7.36c, Rv0938, ligD
Pfam: LigD, primase-polymerase domain
InterPro:
CATH: Alpha-Beta Plaits
Multifunctional non-homologous end joining DNA repair protein LigD in PDB entry 4mky, assembly 1, front view.
Multifunctional non-homologous end joining DNA repair protein LigD in PDB entry 4mky, assembly 1, side view.
Multifunctional non-homologous end joining DNA repair protein LigD in PDB entry 4mky, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P9WNV3  
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DNA chains E, G, I, K
Name: 5'-D(P*DGP*DCP*DGP*DGP*DC)-3'
Representative chains: E, G, I, K
Source organism: Mycobacterium tuberculosis [1773]
Expression system: Not provided
Length: 5 nucleotides
Theoretical weight: 1.52 KDa
5'-D(P*DGP*DCP*DGP*DGP*DC)-3' in PDB entry 4mky, assembly 1, front view.
5'-D(P*DGP*DCP*DGP*DGP*DC)-3' in PDB entry 4mky, assembly 1, side view.
5'-D(P*DGP*DCP*DGP*DGP*DC)-3' in PDB entry 4mky, assembly 1, top view.
151.01.52.02.53.03.54.04.55.0
 
246GCGGC
Chains
Chain E (auth E)
Chain F (auth G)
Chain G (auth I)
Chain H (auth K)
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DNA chains F, H, J, L
Name: 5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DGP*DTP*DAP*DC)-3'
Representative chains: F, H, J, L
Source organism: Mycobacterium tuberculosis [1773]
Expression system: Not provided
Length: 10 nucleotides
Theoretical weight: 3.03 KDa
5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DGP*DTP*DAP*DC)-3' in PDB entry 4mky, assembly 1, front view.
5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DGP*DTP*DAP*DC)-3' in PDB entry 4mky, assembly 1, side view.
5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DGP*DTP*DAP*DC)-3' in PDB entry 4mky, assembly 1, top view.
11012345678910
 
510GCCGCAGTAC
Chains
Chain I (auth F)
Chain J (auth H)
Chain K (auth J)
Chain L (auth L)
Interaction interfaces
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