MolNFT v1 · #38399 · DNA

A D(TGGGGT)- sodium and calcium complex.

2GW0 · 5'-D(*TP*GP*GP*GP*GP*T)-3': “A D(TGGGGT)- sodium and calcium complex.”. X-ray diffraction, 2 ligands (CA, NA), 1 pocket (best druggability 0.34). MolNFT v1 #38399 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2GW0
Type: DNA
Length: 46 nucleotides
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*TP*GP*GP*GP*GP*T)-3'
Ligands: CA, NA
Pockets: 1 · best druggability 0.34

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, E, F, H	5'-D(TPGPGPGPGPT)-3'	dna	6	—	—
C, G	5'-D(TPGPGPGPGPT)-3'	dna	5	—	—

Ligands and binding sites

CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
NA · Sodium ion · metal · 4 copies · chains A, B, C, D, E, F, G, H

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	84	0.34	0.76	9	CA

Interfaces

23 interfaces between chains.

A–B · 355 Å² buried · 15 hydrogen bonds · nucleic-nucleic
E–H · 273 Å² buried · 16 hydrogen bonds · nucleic-nucleic
C–D · 266 Å² buried · 15 hydrogen bonds · nucleic-nucleic
A–D · 256 Å² buried · 15 hydrogen bonds · nucleic-nucleic
B–C · 250 Å² buried · 15 hydrogen bonds · nucleic-nucleic

Compared structures

2GW0 · A D(TGGGGT)- sodium and calcium complex. · 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 2GW0 · PDBe 2GW0

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