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Ferredoxin III from maize root

Analyse Ferredoxin III from maize root in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5H57
Type: protein
Length: 582 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ferredoxin-3, chloroplastic
UniProt: P27788
Ligands: FES
Pockets: 4 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 20% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Ferredoxin-3, chloroplastic	protein	97	20% helix, 33% strand	P27788

Ligands and binding sites

FES · Fe2/s2 (inorganic) cluster · ligand · 6 copies · chains A, B, C, D, E, F

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	1152	0.84	0.85	97	empty
2	393	0.70	0.82	66	empty
3	324	0.64	0.80	31	empty
4	358	0.62	0.78	52	empty

Interfaces

12 interfaces between chains.

D–F · 482 Å² buried · 9 hydrogen bonds · protein-protein
C–E · 477 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 474 Å² buried · 9 hydrogen bonds · protein-protein
A–E · 379 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 379 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5H57 · Ferredoxin III from maize root · the same entry in another collection · chain F against F, TM-score 1.00
P27788 · AlphaFold monomer V2.0 prediction for ferredoxin-3, chloroplastic (P27788) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P27788
Elsewhere: RCSB PDB 5H57 · PDBe 5H57 · UniProt P27788

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