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Crystal structure of mithramycin analogue mtm sa-TRP in complex with a 10-mer DNA agaggcctct.

Analyse Crystal structure of mithramycin analogue mtm sa-TRP in complex with a 10-mer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5JVW
Type
DNA
Length
40 nucleotides
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'-D(*AP*GP*AP*GP*GP*CP*CP*TP*CP*T)-3')
Ligands
6O6, ZN, NA
Pockets
1 · best druggability 0.30

Structure

x-ray diffraction · 1 distinct chain.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, B, C, DDNA (5'-D(*AP*GP*AP*GP*GP*CP*CP*TP*CP*T)-3')dna10——

Ligands and binding sites

  • 6O6 · Plicamycin, mithramycin analogue MTM SA-Trp · ligand · 4 copies · chains A, B, C, D
  • ZN · Zinc ion · metal · 13 copies · chains A, B, D, C
  • NA · Sodium ion · metal · 7 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1970.300.7111ZN

Interfaces

4 interfaces between chains.

  • A–B · 463 Ų buried · 40 hydrogen bonds · nucleic-nucleic
  • C–D · 460 Ų buried · 41 hydrogen bonds · nucleic-nucleic
  • B–D · 21 Ų buried · 0 hydrogen bonds · nucleic-nucleic
  • A–C · 20 Ų buried · 0 hydrogen bonds · nucleic-nucleic

Compared structures

  • 5JVW · Crystal structure of mithramycin analogue MTM SA-Trp in complex with a 10-mer DNA… · the same entry in another collection · chain C against C, TM-score 1.00

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