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Crystal structure of the 2[4FE-4S] ferredoxin from escherichia COLI

Analyse Crystal structure of the 2[4FE-4S] ferredoxin from escherichia COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2ZVS
Type: protein
Length: 241 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized ferredoxin-like protein yfhl
UniProt: P52102
Ligands: SF4
Pockets: 1 · best druggability 0.42

Structure

x-ray diffraction · 2 distinct chains · 25% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Uncharacterized ferredoxin-like protein yfhl	protein	81	25% helix, 12% strand	P52102
B, C	Uncharacterized ferredoxin-like protein yfhl	protein	80	25% helix, 13% strand	P52102

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	169	0.42	0.73	29	empty

Interfaces

3 interfaces between chains.

B–C · 288 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 127 Å² buried · 0 hydrogen bonds · protein-protein
A–B · 11 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2ZVS · Crystal structure of the 2[4FE-4S] ferredoxin from escherichia coli · the same entry in another collection · chain A against A, TM-score 1.00
P52102 · AlphaFold monomer V2.0 prediction for ferredoxin yfhl (P52102) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 P52102
Elsewhere: RCSB PDB 2ZVS · PDBe 2ZVS · UniProt P52102

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