MolNFT v1 · #51888 · protein

3FE-4S, 4FE-4S plus zn acidianus ambivalens ferredoxin

2VKR · Zinc-containing ferredoxin: “3FE-4S, 4FE-4S plus zn acidianus ambivalens ferredoxin”. X-ray diffraction, 3 ligands (F3S, SF4, ZN), 2 pockets (best druggability 0.73). MolNFT v1 #51888 on GenesisL1: 3D structure, binding sites and…

PDB: 2VKR
Type: protein
Length: 721 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Zinc-containing ferredoxin
UniProt: P49949
Ligands: F3S, SF4, ZN
Pockets: 2 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 17% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G	Zinc-containing ferredoxin	protein	103	17% helix, 27% strand	P49949

Ligands and binding sites

F3S · FE3-S4 cluster · ligand · 7 copies · chains A, B, C, D, E, F, G
SF4 · Iron/sulfur cluster · ligand · 7 copies · chains A, B, C, D, E, F, G
ZN · Zinc ion · metal · 7 copies · chains A, B, C, D, E, F, G

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

Pockets

2 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	977	0.73	0.76	79	empty
2	51	0.27	0.74	13	empty

Interfaces

5 interfaces between chains.

E–G · 280 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 257 Å² buried · 5 hydrogen bonds · protein-protein
C–G · 156 Å² buried · 1 hydrogen bond · protein-protein
C–E · 79 Å² buried · 0 hydrogen bonds · protein-protein
A–E · 22 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2VKR · 3Fe-4S, 4Fe-4S plus Zn Acidianus ambivalens ferredoxin · the same entry in another collection · chain G against G, TM-score 1.00
P49949 · AlphaFold monomer V2.0 prediction for zinc-containing ferredoxin (P49949) · 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 P49949
Elsewhere: RCSB PDB 2VKR · PDBe 2VKR · UniProt P49949

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