MolNFT v1 · #140562 · protein

Crystal structure of SO_3166-SO_3165 from shewanella oneidensis

5YEP · Toxin-antitoxin system antidote mnt family: “Crystal structure of SO_3166-SO_3165 from shewanella oneidensis”. X-ray diffraction, 6 pockets (best druggability 0.77). MolNFT v1 #140562 on GenesisL1: 3D structure, binding sites and…

PDB: 5YEP
Type: protein
Length: 517 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Toxin-antitoxin system antidote mnt family; Toxin-antitoxin system toxin hepn family
UniProt: Q8ECH7, Q8ECH6
Pockets: 6 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 66% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Toxin-antitoxin system antidote mnt family	protein	119	50% helix, 20% strand	Q8ECH7
B, D	Toxin-antitoxin system toxin hepn family	protein	133	73% helix, 0% strand	Q8ECH6
C	Toxin-antitoxin system toxin hepn family	protein	132	72% helix, 0% strand	Q8ECH6

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1024	0.77	0.79	102	empty
2	202	0.53	0.78	33	empty
3	178	0.53	0.79	26	empty
4	151	0.49	0.78	23	empty
5	92	0.39	0.77	21	empty

Interfaces

5 interfaces between chains.

B–C · 849 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 759 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 622 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 620 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 191 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 modified (engineered).

Compared structures

5YEP · Crystal structure of SO_3166-SO_3165 from Shewanella oneidensis · the same entry in another collection · chain A against A, TM-score 1.00
Q8ECH6 · AlphaFold monomer V2.0 prediction for mRNA nuclease hept (Q8ECH6) · a predicted model of the same protein · chain B against A, TM-score 0.97
Q8ECH7 · AlphaFold monomer V2.0 prediction for protein adenylyltransferase mnta (Q8ECH7) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 Q8ECH7
Every structure of UniProt Q8ECH6
Elsewhere: RCSB PDB 5YEP · PDBe 5YEP · UniProt Q8ECH7 · UniProt Q8ECH6

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