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MolNFT v1 · #31637 · DNA

5'-D(*GP*CP*AP*GP*AP*CP*GP*TP*CP*TP*GP*C)-3' methionine repressor binding site

2B1D: “5'-D(*GP*CP*AP*GP*AP*CP*GP*TP*CP*TP*GP*C)-3' methionine repressor binding site”. X-ray diffraction, 2 ligands (NCO, MG), 2 pockets (best druggability 0.74). MolNFT v1 #31637 on GenesisL1: 3D structure, binding sites and pockets in…

PDB
2B1D
Type
DNA
Length
72 nucleotides
Chains
6
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-D(*GP*CP*AP*GP*AP*CP*GP*TP*CP*TP*GP*C)-3'
Ligands
NCO, MG
Pockets
2 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, B, C, D, E, F5'-D(*GP*CP*AP*GP*AP*CP*GP*TP*CP*TP*GP*C)-3'dna12——

Ligands and binding sites

  • NCO · Cobalt hexammine(iii) · ligand · 3 copies · chains A, B, C, F, D, E
  • MG · Magnesium ion · metal

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
111800.740.7848NCO
2610.250.7210empty

Interfaces

12 interfaces between chains.

  • C–D · 551 Ų buried · 65 hydrogen bonds · nucleic-nucleic
  • A–B · 549 Ų buried · 62 hydrogen bonds · nucleic-nucleic
  • E–F · 545 Ų buried · 62 hydrogen bonds · nucleic-nucleic
  • A–C · 89 Ų buried · 3 hydrogen bonds · nucleic-nucleic
  • B–D · 81 Ų buried · 0 hydrogen bonds · nucleic-nucleic

Compared structures

  • 2B1D · 5'-D(*GP*CP*AP*GP*AP*CP*GP*TP*CP*TP*GP*C)-3' Methionine Repressor binding site · the same entry in another collection · chain A against A, TM-score 1.00

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