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Yfea oligomer crystal 1, form 1

Analyse Yfea oligomer crystal 1, form 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7ME1
Type: protein
Length: 549 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Periplasmic chelated iron-binding protein yfea
UniProt: Q56952
Ligands: ZN, FE, MN
Pockets: 3 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Periplasmic chelated iron-binding protein yfea	protein	272	46% helix, 15% strand	Q56952
B	Periplasmic chelated iron-binding protein yfea	protein	277	44% helix, 15% strand	Q56952

Ligands and binding sites

ZN · Zinc ion · metal · 3 copies · chains A, B
FE · Fe (III) ion · metal · 2 copies · chains A, B
MN · Manganese (II) ion · metal · chains B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1087	0.71	0.75	89	empty
2	64	0.30	0.74	19	empty
3	53	0.27	0.74	12	empty

Interfaces

1 interface between chains.

A–B · 393 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

7ME1 · YfeA oligomer crystal 1, form 1 · the same entry in another collection · chain A against A, TM-score 1.00
Q56952 · AlphaFold monomer V2.0 prediction for periplasmic chelated iron- binding protein yfea… · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q56952
Elsewhere: RCSB PDB 7ME1 · PDBe 7ME1 · UniProt Q56952

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