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Oxidized (di-ferric) fpra from moorella thermoacetica

Analyse Oxidized (di-ferric) fpra from moorella thermoacetica in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1YCF
Type: protein
Length: 1,592 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nitric oxide reductase
EC: 1.-.-.-
UniProt: Q9FDN7
Ligands: FEO, FMN, ZN, OXY
Pockets: 11 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Nitric oxide reductase (EC 1.-.-.-)	protein	398	37% helix, 23% strand	Q9FDN7

Ligands and binding sites

FEO · Mu-oxo-diiron · ligand · 4 copies · chains A, B, C, D
FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
ZN · Zinc ion · metal · 3 copies · chains A, B
OXY · Oxygen molecule · ion · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	358	0.78	0.88	48	FMN
2	397	0.77	0.86	55	FMN
3	313	0.76	0.88	44	FMN
4	347	0.76	0.87	48	FMN
5	410	0.65	0.78	33	empty

Interfaces

3 interfaces between chains.

A–B · 1698 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 1688 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 381 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

1YCF · Oxidized (di-ferric) FprA from Moorella thermoacetica · the same entry in another collection · chain D against D, TM-score 1.00
Q9FDN7 · AlphaFold monomer V2.0 prediction for nitric oxide reductase (Q9FDN7) · a predicted model of the same protein · chain C 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 Q9FDN7
Elsewhere: RCSB PDB 1YCF · PDBe 1YCF · UniProt Q9FDN7

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