GL1X · GenesisL1 explorer

MolNFT v1 · #16933 · protein + DNA

Structure of the gcm domain bound to DNA

1ODH · MGCM1: “Structure of the gcm domain bound to DNA”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.65). MolNFT v1 #16933 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
1ODH
Type
protein + DNA
Length
183 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
MGCM1; 5'-D(*CP*GP*AP*TP*GP*CP*GP*GP*GP*TP *GP*CP*A)-3'…
UniProt
P70348
Ligands
ZN
Pockets
3 · best druggability 0.65

Structure

x-ray diffraction · 3 distinct chains · 13% helix, 25% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AMGCM1protein15713% helix, 25% strandP70348
C5'-D(*CP*GP*AP*TP*GP*CP*GP*GP*GP*TP *GP*CP*A)-3'dna13——
D5'-D(*TP*GP*CP*AP*CP*CP*CP*GP*CP*AP *TP*CP*G)-3'dna13——

Ligands and binding sites

  • ZN · Zinc ion · metal · 2 copies · chains A

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
13370.650.8026empty
21660.600.8325empty
31440.500.7925empty

Interfaces

3 interfaces between chains.

  • A–C · 653 Ų buried · 18 hydrogen bonds · protein-nucleic
  • C–D · 598 Ų buried · 44 hydrogen bonds · nucleic-nucleic
  • A–D · 336 Ų buried · 4 hydrogen bonds · protein-nucleic

Compared structures

  • 1ODH · Structure of the GCM domain bound to DNA · the same entry in another collection · chain A against A, TM-score 1.00
  • P70348 · AlphaFold monomer V2.0 prediction for chorion-specific transcription factor gcma (P70348) · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.