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Crystal structure of NAF1 (MINER1): H114C the redox-active 2FE-2S protein

Analyse Crystal structure of NAF1 (MINER1): H114C the redox-active 2FE-2S protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4OOA
Type: protein
Length: 392 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cdgsh iron-sulfur domain-containing protein 2
UniProt: Q8N5K1
Ligands: FES
Pockets: 2 · best druggability 0.70

Structure

x-ray diffraction · 5 distinct chains · 18% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cdgsh iron-sulfur domain-containing protein 2	protein	66	18% helix, 23% strand	Q8N5K1
B	Cdgsh iron-sulfur domain-containing protein 2	protein	66	18% helix, 24% strand	Q8N5K1
C, D	Cdgsh iron-sulfur domain-containing protein 2	protein	64	19% helix, 28% strand	Q8N5K1
E	Cdgsh iron-sulfur domain-containing protein 2	protein	65	18% helix, 20% strand	Q8N5K1
F	Cdgsh iron-sulfur domain-containing protein 2	protein	67	18% helix, 19% strand	Q8N5K1

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

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	787	0.70	0.76	73	empty
2	180	0.47	0.75	27	empty

Interfaces

9 interfaces between chains.

E–F · 1946 Å² buried · 46 hydrogen bonds · protein-protein
A–B · 1848 Å² buried · 53 hydrogen bonds · protein-protein
C–D · 1760 Å² buried · 45 hydrogen bonds · protein-protein
B–C · 631 Å² buried · 9 hydrogen bonds · protein-protein
B–F · 518 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

4OOA · CRYSTAL STRUCTURE of NAF1 (MINER1): H114C THE REDOX-ACTIVE 2FE-2S PROTEIN · the same entry in another collection · chain F against F, TM-score 1.00
Q8N5K1 · AlphaFold monomer V2.0 prediction for cdgsh iron-sulfur domain- containing protein 2… · a predicted model of the same protein · chain C against A, TM-score 0.98

Analyse

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Every structure of UniProt Q8N5K1
Elsewhere: RCSB PDB 4OOA · PDBe 4OOA · UniProt Q8N5K1

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