MolNFT v1 · #31636 · DNA

5'-D(GPCPGPTPGPGPGPAPCPC)-3' ZIF268 binding site

2B1C: “5'-D(*GP*CP*GP*TP*GP*GP*GP*AP*CP*C)-3' ZIF268 binding site”. X-ray diffraction, 1 ligand (MG), 1 pocket (best druggability 0.36). MolNFT v1 #31636 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2B1C
Type: DNA
Length: 20 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*GP*CP*GP*TP*GP*GP*GP*AP*CP*C)-3'; 5'-D(*GP*GP*TP*CP*CP*CP*AP*CP*GP*C)-3'
Ligands: MG
Pockets: 1 · best druggability 0.36

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5'-D(GPCPGPTPGPGPGPAPCPC)-3'	dna	10	—	—
B	5'-D(GPGPTPCPCPCPAPCPGPC)-3'	dna	10	—	—

Ligands and binding sites

MG · Magnesium ion · metal · chains A

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	129	0.36	0.73	11	empty

Interfaces

1 interface between chains.

A–B · 461 Å² buried · 46 hydrogen bonds · nucleic-nucleic

Compared structures

2B1C · 5'-D(*GP*CP*GP*TP*GP*GP*GP*AP*CP*C)-3' Zif268 binding site · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 2B1C · PDBe 2B1C

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