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Hyperthermophile chromosomal protein SAC7D double mutant VAL26ALA/MET29ALA in complex with DNA gcgatcgc

Analyse Hyperthermophile chromosomal protein SAC7D double mutant VAL26ALA/MET29ALA in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
1XYI
Type
protein + DNA
Length
82 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3'; DNA-binding proteins 7A/7B/7D
UniProt
P13123
Pockets
1 · best druggability 0.42

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 53% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
B, C5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3'dna8——
ADNA-binding proteins 7A/7B/7Dprotein6626% helix, 53% strandP13123

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11070.420.7814empty

Interfaces

3 interfaces between chains.

  • C–A · 393 Ų buried · 2 hydrogen bonds · protein-nucleic
  • B–C · 378 Ų buried · 33 hydrogen bonds · nucleic-nucleic
  • B–A · 378 Ų buried · 7 hydrogen bonds · protein-nucleic

Compared structures

  • 1XYI · Hyperthermophile chromosomal protein Sac7d double mutant Val26Ala/Met29Ala in complex… · the same entry in another collection · chain B against B, TM-score 1.00
  • P13123 · AlphaFold monomer V2.0 prediction for DNA-binding protein 7D (P13123) · a predicted model of the same protein · chain A against A, TM-score 0.93

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