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Structure of fesii (shethna) protein from azotobacter vinelandii

Analyse Structure of fesii (shethna) protein from azotobacter vinelandii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YAV
Type: protein
Length: 585 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dimeric (2FE-2S) protein
UniProt: Q44501
Ligands: FES, MG
Pockets: 6 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 20% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	Dimeric (2FE-2S) protein	protein	109	17% helix, 27% strand	Q44501
A, B, C, D	Dimeric (2FE-2S) protein	protein	119	23% helix, 25% strand	Q44501

Ligands and binding sites

FES · Fe2/s2 (inorganic) cluster · ligand · 5 copies · chains E, A, B, C, D
MG · Magnesium ion · metal · chains E
GOL · Glycerol · additive · 2 copies · chains E, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	601	0.78	0.83	71	empty
2	442	0.68	0.80	56	GOL
3	366	0.62	0.78	45	FES
4	67	0.38	0.78	15	empty
5	50	0.35	0.80	22	empty

Interfaces

7 interfaces between chains.

A–B · 1229 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 1038 Å² buried · 9 hydrogen bonds · protein-protein
E–B · 342 Å² buried · 5 hydrogen bonds · protein-protein
E–D · 335 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 138 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6YAV · Structure of FeSII (Shethna) protein from Azotobacter vinelandii · the same entry in another collection · chain D against D, TM-score 1.00
Q44501 · AlphaFold monomer V2.0 prediction for protein fesii (Q44501) · a predicted model of the same protein · chain E against A, TM-score 0.86

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 Q44501
Elsewhere: RCSB PDB 6YAV · PDBe 6YAV · UniProt Q44501

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