MolNFT v1 · #124112 · protein + DNA

Structure of aspa-26MER DNA complex

5K5O: “Structure of aspa-26MER DNA complex”. X-ray diffraction, 8 pockets (best druggability 0.59). MolNFT v1 #124112 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5K5O
Type: protein + DNA
Length: 415 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aspa; DNA (26-mer)
UniProt: O93706
Pockets: 8 · best druggability 0.59

Structure

x-ray diffraction · 5 distinct chains · 52% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Aspa	protein	92	50% helix, 10% strand	O93706
B	Aspa	protein	91	49% helix, 15% strand	O93706
C	Aspa	protein	88	57% helix, 11% strand	O93706
N	DNA (26-mer)	dna	26	—	—
M	DNA (26-mer)	dna	26	—	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	258	0.59	0.80	22	empty
2	85	0.36	0.76	15	empty
3	84	0.34	0.74	13	empty
4	72	0.31	0.74	14	empty
5	63	0.31	0.75	16	empty

Interfaces

12 interfaces between chains.

A–B · 1585 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 1457 Å² buried · 10 hydrogen bonds · protein-protein
N–M · 1143 Å² buried · 97 hydrogen bonds · nucleic-nucleic
B–M · 565 Å² buried · 8 hydrogen bonds · protein-nucleic
D–M · 547 Å² buried · 10 hydrogen bonds · protein-nucleic

Compared structures

5K5O · Structure of AspA-26mer DNA 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
Every structure of UniProt O93706
Elsewhere: RCSB PDB 5K5O · PDBe 5K5O · UniProt O93706

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