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Mfd DNA complex

Analyse Mfd DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
7SSG
Type
protein + DNA
Length
429 residues
Chains
3
Method
electron microscopy
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Transcription-repair-coupling factor; DNA (5'-D(P*TP*TP*GP*CP*CP*TP*CP*GP*CP*TP*GP*CP*CP*A…
EC
3.6.4.-
UniProt
P30958
Pockets
9 · best druggability 0.88

Structure

electron microscopy · 3 distinct chains · 36% helix, 9% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ATranscription-repair-coupling factor (EC 3.6.4.-)protein38236% helix, 9% strandP30958
BDNA (5'-D(P*TP*TP*GP*CP*CP*TP*CP*GP*CP*TP*GP*CP*CP*A)-3')dna29——
CDNA (5'-D(P*TP*GP*GP*CP*GP*GP*CP*GP*AP*GP*GP*C)-3')dna18——

Pockets

9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
19460.880.90123empty
211000.830.8479empty
32610.760.8950empty
42620.650.8249empty
5610.510.8617empty

Interfaces

3 interfaces between chains.

  • B–C · 1065 Ų buried · 75 hydrogen bonds · nucleic-nucleic
  • A–B · 637 Ų buried · 6 hydrogen bonds · protein-nucleic
  • A–C · 468 Ų buried · 8 hydrogen bonds · protein-nucleic

Compared structures

  • 7SSG · Mfd DNA complex · the same entry in another collection · chain A against A, TM-score 1.00
  • P30958 · AlphaFold monomer V2.0 prediction for transcription-repair-coupling factor (P30958) · a predicted model of the same protein · chain A against A, TM-score 0.85

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