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MolNFT v1 · #169518 · protein + DNA

Structure of mfd bound to dsdna

6XEO · Transcription-repair-coupling factor: “Structure of mfd bound to dsdna”. Electron microscopy, 18 pockets (best druggability 0.89). MolNFT v1 #169518 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
6XEO
Type
protein + DNA
Length
1,154 residues
Chains
3
Method
electron microscopy
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Transcription-repair-coupling factor; DNA (5'…
EC
3.6.4.-
UniProt
P30958
Pockets
18 · best druggability 0.89

Structure

electron microscopy · 3 distinct chains · 37% helix, 10% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ATranscription-repair-coupling factor (EC 3.6.4.-)protein111837% helix, 10% strandP30958
BDNA (5'- D(P*AP*GP*GP*AP*TP*AP*CP*TP*TP*AP*CP*AP*GP*CP*CP*AP*TP*C)-3')dna18——
CDNA (5'- D(P*GP*AP*TP*GP*GP*CP*TP*GP*TP*AP*AP*GP*TP*AP*TP*CP*CP*T)-3')dna18——

Pockets

18 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
110320.890.91138empty
26800.870.91106empty
35020.850.9169empty
49270.850.8688empty
59150.840.8599empty

Interfaces

3 interfaces between chains.

  • B–C · 936 Ų buried · 80 hydrogen bonds · nucleic-nucleic
  • A–C · 410 Ų buried · 8 hydrogen bonds · protein-nucleic
  • A–B · 236 Ų buried · 4 hydrogen bonds · protein-nucleic

Compared structures

  • 6XEO · Structure of Mfd bound to dsDNA · 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 0.64

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