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ternary complex of DNA polymerase SFM4-3 recognizing C2 methyoxy nucleotide

X-ray diffraction
2.4Å resolution
PDB entry 8xk9 coloured by chain, front view.
PDB entry 8xk9 coloured by chain, side view.
PDB entry 8xk9 coloured by chain, top view.
Source organisms:
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: DNA polymerase I, thermostable and DNA
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Multimeric state: hetero hexamer
Accessible surface area: 49422.52 Å2
Buried surface area: 14414.05 Å2
Dissociation area: 956.2 Å2
Dissociation energy (ΔGdiss): -12.13 kcal/mol
Dissociation entropy (TΔSdiss): 15.1 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-283120

Macromolecules

DNA polymerase I, thermostable
Chains: A, D
Length: 539 amino acids
Theoretical weight: 60.8 KDa
Source organism: Thermus aquaticus
Expression system: Escherichia coli
UniProt:
  • Canonical: P52028 (Residues: 296-833; Coverage: 65%)
Gene names: TTHA1054, polA
Pfam:
DNA polymerase I, thermostable in PDB entry 8xk9, assembly 1, front view.
DNA polymerase I, thermostable in PDB entry 8xk9, assembly 1, side view.
DNA polymerase I, thermostable in PDB entry 8xk9, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P52028  
153950100150200250300350400450500
 
200400MEEAPWPPPEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKALRDLKEARGLLAKDLSVLALREGLGLPPGDDPMLLAYLLDPSNTTPEGVARRYGGEWTEEAGERAALSERLFANLWGRLEGEERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPFNLNSRDQLERVLFDELGLPAIGKTEKTGKRSTSAAALEALREAHPIVEKILQYRELTKLKSTYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQSIPVRTPLGQRIRRAFIAEEGWLLVALDYSQEGLRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVNPLMRRAAKTINFGVLYGMSAHRLSQKLAIPYEEAQAFIERYFQSFPKVRAWIEKTLEEGRRRGYVETLFGRRRYVPDLEARVKSVRQAAERRAFNMPVQGTAADLMKLAMVKLFPRLEEMGARMLLQVHDELVLEAPKERAEAVARLAKEVMEGVYPLAVPLEVEVGIGEDWLSAKE
UniProt
P52028
Chains
Ligand binding sites
Interaction interfaces
Sequence conservation
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DNA chains B, E
Name: DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3')
Representative chains: B, E
Source organism: synthetic construct [32630]
Expression system: Not provided
Length: 12 nucleotides
Theoretical weight: 3.62 KDa
DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3') in PDB entry 8xk9, assembly 1, front view.
DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3') in PDB entry 8xk9, assembly 1, side view.
DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3') in PDB entry 8xk9, assembly 1, top view.
112123456789101112
 
510GACCACGGCGC*
Chains
Chain A (auth B)
Chain D (auth E)
Ligand binding sites
Interaction interfaces
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DNA chains C, F
Name: DNA (5'-D(*AP*AP*CP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-R(P*(OMG))-3')
Representative chains: C, F
Source organism: synthetic construct [32630]
Expression system: Not provided
Length: 16 nucleotides
Theoretical weight: 4.97 KDa
DNA (5'-D(*AP*AP*CP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-R(P*(OMG))-3') in PDB entry 8xk9, assembly 1, front view.
DNA (5'-D(*AP*AP*CP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-R(P*(OMG))-3') in PDB entry 8xk9, assembly 1, side view.
DNA (5'-D(*AP*AP*CP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-R(P*(OMG))-3') in PDB entry 8xk9, assembly 1, top view.
116246810121416
 
51015
Chains
Chain B (auth C)
Chain E (auth F)
Ligand binding sites
Interaction interfaces
Molecule details ›

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