MolNFT v1 · #155465 · protein + DNA

Crystal structure of heterohexameric yoeb-yefm complex bound to 26BP- DNA

6L8E · Yefm antitoxin: “Crystal structure of heterohexameric yoeb-yefm complex bound to 26BP- DNA”. X-ray diffraction, 14 pockets (best druggability 0.86). MolNFT v1 #155465 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6L8E
Type: protein + DNA
Length: 996 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yefm antitoxin; Yoeb toxin; DNA (26-mer)
UniProt: Q2G285, Q2G286
Pockets: 14 · best druggability 0.86

Structure

x-ray diffraction · 9 distinct chains · 49% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, I, K	Yefm antitoxin	protein	83	55% helix, 23% strand	Q2G285
B	Yefm antitoxin	protein	54	52% helix, 26% strand	Q2G285
D	Yefm antitoxin	protein	55	51% helix, 24% strand	Q2G285
E, F, M, N	Yoeb toxin	protein	87	38% helix, 29% strand	Q2G286
G, O	DNA (26-mer)	dna	23	—	—
H	DNA (26-mer)	dna	22	—	—
J	Yefm antitoxin	protein	59	53% helix, 24% strand	Q2G285
L	Yefm antitoxin	protein	57	51% helix, 25% strand	Q2G285
P	DNA (26-mer)	dna	23	—	—

Pockets

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	587	0.86	0.92	44	empty
2	689	0.86	0.90	48	empty
3	735	0.75	0.80	77	empty
4	579	0.66	0.77	73	empty
5	491	0.65	0.77	44	empty

Interfaces

58 interfaces between chains.

K–N · 1735 Å² buried · 28 hydrogen bonds · protein-protein
A–E · 1732 Å² buried · 27 hydrogen bonds · protein-protein
C–F · 1682 Å² buried · 27 hydrogen bonds · protein-protein
I–M · 1674 Å² buried · 26 hydrogen bonds · protein-protein
K–L · 1568 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

6L8E · Crystal structure of heterohexameric YoeB-YefM complex bound to 26bp-DNA · the same entry in another collection · chain P against P, 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 Q2G285
Every structure of UniProt Q2G286
Elsewhere: RCSB PDB 6L8E · PDBe 6L8E · UniProt Q2G285 · UniProt Q2G286

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