MolNFT v1 · #115456 · protein

E.COLI mazf E24A form iia

5CKE · Endoribonuclease mazf: “E.COLI mazf E24A form iia”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.39). MolNFT v1 #115456 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5CKE
Type: protein
Length: 212 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endoribonuclease mazf
EC: 3.1.27.-
UniProt: P0AE70
Ligands: SO4
Pockets: 2 · best druggability 0.39

Structure

x-ray diffraction · 2 distinct chains · 23% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Endoribonuclease mazf (EC 3.1.27.-)	protein	101	22% helix, 29% strand	P0AE70
B	Endoribonuclease mazf (EC 3.1.27.-)	protein	111	23% helix, 32% strand	P0AE70

Ligands and binding sites

SO4 · Sulfate ion · ion · chains B
MRD · (4R)-2-methylpentane-2,4-diol · additive · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	93	0.39	0.76	22	MRD
2	67	0.31	0.75	16	empty

Interfaces

1 interface between chains.

A–B · 899 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5CKE · E.coli MazF E24A form IIa · the same entry in another collection · chain A against A, TM-score 1.00
P0AE70 · AlphaFold monomer V2.0 prediction for endoribonuclease toxin mazf (P0AE70) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 5CKE · PDBe 5CKE · UniProt P0AE70

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