MolNFT v1 · #175836 · DNA

The PB2+ complexed structure of tba G8C mutant

7D33 · DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*CP*TP*GP*GP*TP*TP*GP*G)- 3'): “The PB2+ complexed structure of tba G8C mutant”. X-ray diffraction, 1 ligand (PB), 1 pocket (best druggability 0.32). MolNFT v1 #175836 on GenesisL1: 3D structure…

PDB: 7D33
Type: DNA
Length: 75 nucleotides
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*CP*TP*GP*GP*TP*TP*GP*G)- 3')
Ligands: PB
Pockets: 1 · best druggability 0.32

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	DNA (5'-D(GPGPTPTPGPGPTPCPTPGPGPTPTPGP*G)- 3')	dna	15	—	—

Ligands and binding sites

PB · Lead (II) ion · metal · 5 copies · chains A, B, C, D, E

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	65	0.32	0.76	10	empty

Interfaces

5 interfaces between chains.

C–D · 739 Å² buried · 30 hydrogen bonds · nucleic-nucleic
A–B · 738 Å² buried · 29 hydrogen bonds · nucleic-nucleic
A–E · 318 Å² buried · 4 hydrogen bonds · nucleic-nucleic
B–E · 47 Å² buried · 0 hydrogen bonds · nucleic-nucleic
C–E · 11 Å² buried · 0 hydrogen bonds · nucleic-nucleic

Compared structures

7D33 · The Pb2+ complexed structure of TBA G8C mutant · 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 7D33 · PDBe 7D33

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