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MolNFT v1 · #128957 · protein + DNA

Crystal structure of ubalai restriction endonuclease B3 domain domain (mutant L24M L53M L95M) with cognate DNA

5O63 · Restriction endonuclease ubalai: “Crystal structure of ubalai restriction endonuclease B3 domain domain (mutant L24M L53M L95M) with cognate DNA”. X-ray diffraction, 1 pocket (best druggability 0.60). MolNFT v1 #128957 on GenesisL1…

PDB
5O63
Type
protein + DNA
Length
356 residues
Chains
6
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Restriction endonuclease ubalai; DNA (5'-D(*C*G*C*C*A*G*G*G*C*)-3'); DNA…
EC
3.1.21.4
Pockets
1 · best druggability 0.60

Structure

x-ray diffraction · 4 distinct chains · 19% helix, 36% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ARestriction endonuclease ubalai (EC 3.1.21.4)protein15919% helix, 36% strand—
BRestriction endonuclease ubalai (EC 3.1.21.4)protein16119% helix, 36% strand—
C, EDNA (5'-D(*C*G*C*C*A*G*G*G*C*)-3')dna9——
D, FDNA (5'-D(*G*C*C*C*T*G*G*C*G*)-3')dna9——

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
13970.600.7657empty

Interfaces

11 interfaces between chains.

  • B–F · 516 Ų buried · 14 hydrogen bonds · protein-nucleic
  • A–D · 510 Ų buried · 13 hydrogen bonds · protein-nucleic
  • A–C · 509 Ų buried · 17 hydrogen bonds · protein-nucleic
  • B–E · 508 Ų buried · 17 hydrogen bonds · protein-nucleic
  • C–D · 439 Ų buried · 36 hydrogen bonds · nucleic-nucleic

Compared structures

  • 5O63 · Crystal structure of UbaLAI restriction endonuclease B3 domain domain (mutant L24M L53M… · the same entry in another collection · chain A against A, TM-score 1.00

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