MolNFT v1 · #38032 · protein + DNA

Structural insight into self-sacrifice mechanism of enediyne resistance

2GKD · 5'-D(*GP*CP*AP*TP*AP*TP*GP*AP*TP*AP*G)-3': “Structural insight into self-sacrifice mechanism of enediyne resistance”. Solution nmr, 2 pockets (best druggability 0.71). MolNFT v1 #38032 on GenesisL1: 3D structure, binding sites and…

PDB: 2GKD
Type: protein + DNA
Length: 177 residues
Chains: 3
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*GP*CP*AP*TP*AP*TP*GP*AP*TP*AP*G)-3'; 5'-D(*CP*TP*AP*TP*CP*AP*TP*AP*TP*GP*C)-3'; Calc
UniProt: Q8KNF0
Pockets: 2 · best druggability 0.71

Structure

solution nmr · 3 distinct chains · 24% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	5'-D(GPCPAPTPAPTPGPAPTPAP*G)-3'	dna	11	—	—
C	5'-D(CPTPAPTPCPAPTPAPTPGP*C)-3'	dna	11	—	—
A	Calc	protein	155	24% helix, 31% strand	Q8KNF0

Pockets

2 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	204	0.71	0.87	28	empty
2	112	0.43	0.78	16	empty

Interfaces

3 interfaces between chains.

B–C · 482 Å² buried · 57 hydrogen bonds · nucleic-nucleic
B–A · 211 Å² buried · 3 hydrogen bonds · protein-nucleic
C–A · 197 Å² buried · 4 hydrogen bonds · protein-nucleic

Compared structures

2GKD · Structural insight into self-sacrifice mechanism of enediyne resistance · the same entry in another collection · chain B against B, 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 Q8KNF0
Elsewhere: RCSB PDB 2GKD · PDBe 2GKD · UniProt Q8KNF0

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