Research workbench

Ferredoxin I from C. reinhardtii, low X-ray dose

Analyse Ferredoxin I from C. reinhardtii, low X-ray dose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6KUM
Type: protein
Length: 189 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ferredoxin, chloroplastic
UniProt: P07839
Ligands: BEN, FES, NA, CL, SCN
Pockets: 1 · best druggability 0.28

Structure

x-ray diffraction · 2 distinct chains · 20% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ferredoxin, chloroplastic	protein	94	19% helix, 34% strand	P07839
B	Ferredoxin, chloroplastic	protein	95	20% helix, 34% strand	P07839

Ligands and binding sites

BEN · Benzamidine · ligand · 3 copies · chains A, B
FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, B
NA · Sodium ion · metal · chains B
CL · Chloride ion · ion · 2 copies · chains B
SCN · Thiocyanate ion · ion · chains B

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	56	0.28	0.74	15	empty

Interfaces

1 interface between chains.

A–B · 403 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

6KUM · Ferredoxin I from C. reinhardtii, low X-ray dose · the same entry in another collection · chain A against A, TM-score 1.00
P07839 · AlphaFold monomer V2.0 prediction for ferredoxin, chloroplastic (P07839) · 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 P07839
Elsewhere: RCSB PDB 6KUM · PDBe 6KUM · UniProt P07839

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