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Crystal structure of PacI-DNA Enzyme product complex

X-ray diffraction
1.92Å resolution
PDB entry 3m7k coloured by chain, front view.
PDB entry 3m7k coloured by chain, side view.
PDB entry 3m7k coloured by chain, top view.
Source organism: Aquipseudomonas alcaligenes
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: Restriction endonuclease PacI and DNA
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Multimeric state: hetero hexamer
Accessible surface area: 15166.26 Å2
Buried surface area: 14237.75 Å2
Dissociation area: 2,803.01 Å2
Dissociation energy (ΔGdiss): 39.31 kcal/mol
Dissociation entropy (TΔSdiss): 20.12 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-112712

Macromolecules

Restriction endonuclease PacI
Chain: A
Length: 142 amino acids
Theoretical weight: 15.78 KDa
Source organism: Pseudomonas alcaligenes
Expression system: Pseudomonas alcaligenes
UniProt:
  • Canonical: D5MNX7 (Residues: 1-142; Coverage: 100%)
Gene name: pacIR
CATH: Herpes Virus-1
Restriction endonuclease PacI in PDB entry 3m7k, assembly 1, front view.
Restriction endonuclease PacI in PDB entry 3m7k, assembly 1, side view.
Restriction endonuclease PacI in PDB entry 3m7k, assembly 1, top view.
PDBe-KB: UniProt Coverage View: D5MNX7  
1142102030405060708090100110120130140
 
50100MTQCPRCQRNLAADEFYAGSSKMCKGCMTWQNLSYNANKEGHANTFTKATFLAWYGLSAQRHCGYCGISEAGFTSLHRTNPRGYHIQCLGVDRSDSFEGYSPQNARLACFICNRIKSNIFSASEMDVLGEAISKAWHGRGIA
UniProt
D5MNX7
Chains
Domains
Secondary structure
Flexibility predictions
Early folding residue predictions
Ligand binding sites
Interaction interfaces
Sequence conservation
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DNA chain B
Name: DNA (5'-D(*GP*AP*GP*GP*CP*TP*TP*AP*AP*T)-3')
Representative chains: B
Source organism: Aquipseudomonas alcaligenes [43263]
Expression system: Not provided
Length: 10 nucleotides
Theoretical weight: 3.08 KDa
DNA (5'-D(*GP*AP*GP*GP*CP*TP*TP*AP*AP*T)-3') in PDB entry 3m7k, assembly 1, front view.
DNA (5'-D(*GP*AP*GP*GP*CP*TP*TP*AP*AP*T)-3') in PDB entry 3m7k, assembly 1, side view.
DNA (5'-D(*GP*AP*GP*GP*CP*TP*TP*AP*AP*T)-3') in PDB entry 3m7k, assembly 1, top view.
11012345678910
 
510GAGGCTTAAT
Chains
RSRZ Outlier Chain B (auth B)
Chain B (auth B)
Ligand binding sites
Interaction interfaces
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DNA chain C
Name: DNA (5'-D(P*TP*AP*AP*GP*CP*CP*TP*C)-3')
Representative chains: C
Source organism: Aquipseudomonas alcaligenes [43263]
Expression system: Not provided
Length: 8 nucleotides
Theoretical weight: 2.39 KDa
DNA (5'-D(P*TP*AP*AP*GP*CP*CP*TP*C)-3') in PDB entry 3m7k, assembly 1, front view.
DNA (5'-D(P*TP*AP*AP*GP*CP*CP*TP*C)-3') in PDB entry 3m7k, assembly 1, side view.
DNA (5'-D(P*TP*AP*AP*GP*CP*CP*TP*C)-3') in PDB entry 3m7k, assembly 1, top view.
181.01.52.02.53.03.54.04.55.05.56.06.57.07.58.0
 
2468TAAGCCTC
Chains
Chain C (auth C)
Ligand binding sites
Interaction interfaces
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