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Structure of C. crescentus gapr-DNA

Analyse Structure of C. crescentus gapr-DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
6CG8
Type
protein + DNA
Length
331 residues
Chains
6
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
UPF0335 protein B7Z12_12435; DNA (5'-D(*TP*TP*AP*AP*AP*AP*TP*TP*AP*AP*A)-3'); DNA…
UniProt
A0A258D3B4
Pockets
3 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 84% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, B, DUPF0335 protein B7Z12_12435protein7784% helix, 0% strandA0A258D3B4
EUPF0335 protein B7Z12_12435protein7883% helix, 0% strandA0A258D3B4
CDNA (5'-D(*TP*TP*AP*AP*AP*AP*TP*TP*AP*AP*A)-3')dna11——
FDNA (5'-D(*TP*TP*TP*AP*AP*TP*TP*TP*TP*AP*A)-3')dna11——

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
18240.760.8050empty
26570.710.7958empty
35990.700.7838empty

Interfaces

13 interfaces between chains.

  • D–E · 1417 Ų buried · 11 hydrogen bonds · protein-protein
  • A–B · 1414 Ų buried · 8 hydrogen bonds · protein-protein
  • A–E · 927 Ų buried · 7 hydrogen bonds · protein-protein
  • B–D · 903 Ų buried · 8 hydrogen bonds · protein-protein
  • C–F · 491 Ų buried · 34 hydrogen bonds · nucleic-nucleic

Compared structures

  • 6CG8 · Structure of C. crescentus GapR-DNA · the same entry in another collection · chain A against A, TM-score 1.00

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