MolNFT v1 · #173893 · protein

Escherichia COLI ytfe (mn)

7BE8 · Iron-sulfur cluster repair protein ytfe: “Escherichia COLI ytfe (mn)”. X-ray diffraction, 3 ligands (MN, O, SO4), 4 pockets (best druggability 0.64). MolNFT v1 #173893 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7BE8
Type: protein
Length: 435 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Iron-sulfur cluster repair protein ytfe
UniProt: P69506
Ligands: MN, O, SO4
Pockets: 4 · best druggability 0.64

Structure

x-ray diffraction · 2 distinct chains · 71% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Iron-sulfur cluster repair protein ytfe	protein	219	73% helix, 1% strand	P69506
B	Iron-sulfur cluster repair protein ytfe	protein	216	69% helix, 1% strand	P69506

Ligands and binding sites

MN · Manganese (II) ion · metal · 4 copies · chains A, B
O · Oxygen atom · ion · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains A
GOL · Glycerol · additive · 4 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	632	0.64	0.75	70	GOL
2	176	0.56	0.80	19	empty
3	202	0.54	0.79	24	empty
4	193	0.52	0.78	28	empty

Interfaces

1 interface between chains.

A–B · 86 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

7BE8 · Escherichia coli YtfE (Mn) · the same entry in another collection · chain A against A, TM-score 1.00
P69506 · AlphaFold monomer V2.0 prediction for iron-sulfur cluster repair protein ytfe (P69506) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P69506
Elsewhere: RCSB PDB 7BE8 · PDBe 7BE8 · UniProt P69506

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