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MolNFT v1 · #26036 · protein + DNA

Crystal structures of the hyperthermophilic chromosomal protein SAC7D in complex with DNA decamers

1WD1 · 5'-D(*CP*CP*TP*AP*CP*GP*TP*AP*GP*G)-3': “Crystal structures of the hyperthermophilic chromosomal protein SAC7D in complex with DNA decamers”. X-ray diffraction, 1 pocket (best druggability 0.29). MolNFT v1 #26036 on GenesisL1: 3D…

PDB
1WD1
Type
protein + DNA
Length
82 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-D(*CP*CP*TP*AP*CP*GP*TP*AP*GP*G)-3'; DNA-binding proteins 7A/7B/7D
UniProt
P13123
Pockets
1 · best druggability 0.29

Structure

x-ray diffraction · 3 distinct chains · 23% helix, 52% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
B5'-D(*CP*CP*TP*AP*CP*GP*TP*AP*GP*G)-3'dna9——
C5'-D(*CP*CP*TP*AP*CP*GP*TP*AP*GP*G)-3'dna9——
ADNA-binding proteins 7A/7B/7Dprotein6423% helix, 52% strandP13123

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1620.290.7414empty

Interfaces

3 interfaces between chains.

  • C–A · 446 Ų buried · 4 hydrogen bonds · protein-nucleic
  • B–A · 433 Ų buried · 10 hydrogen bonds · protein-nucleic
  • B–C · 381 Ų buried · 35 hydrogen bonds · nucleic-nucleic

Compared structures

  • 1WD1 · Crystal structures of the hyperthermophilic chromosomal protein Sac7d in complex with DNA… · 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 0.96

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