MolNFT v1 · #72666 · protein

Crystal structure of E.COLI mazf toxin

3NFC · Pemk-like protein 1: “Crystal structure of E.COLI mazf toxin”. X-ray diffraction, 7 pockets (best druggability 0.56). MolNFT v1 #72666 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3NFC
Type: protein
Length: 559 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pemk-like protein 1
UniProt: P0AE70
Pockets: 7 · best druggability 0.56

Structure

x-ray diffraction · 4 distinct chains · 27% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Pemk-like protein 1	protein	94	27% helix, 30% strand	P0AE70
B	Pemk-like protein 1	protein	92	27% helix, 30% strand	P0AE70
C, D	Pemk-like protein 1	protein	93	27% helix, 30% strand	P0AE70
F	Pemk-like protein 1	protein	93	27% helix, 30% strand	P0AE70

Pockets

7 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	315	0.56	0.76	36	empty
2	333	0.56	0.75	45	empty
3	238	0.54	0.77	21	empty
4	68	0.37	0.78	15	empty
5	71	0.34	0.76	16	empty

Interfaces

6 interfaces between chains.

B–C · 809 Å² buried · 5 hydrogen bonds · protein-protein
D–E · 795 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 281 Å² buried · 0 hydrogen bonds · protein-protein
C–F · 127 Å² buried · 1 hydrogen bond · protein-protein
A–D · 118 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

3NFC · Crystal structure of E.coli MazF Toxin · the same entry in another collection · chain F against F, TM-score 1.00
P0AE70 · AlphaFold monomer V2.0 prediction for endoribonuclease toxin mazf (P0AE70) · a predicted model of the same protein · chain C 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 P0AE70
Elsewhere: RCSB PDB 3NFC · PDBe 3NFC · UniProt P0AE70

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