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Crystal structure of the flavoprotein nrdi from aerococcus urinae in oxidized form

Analyse Crystal structure of the flavoprotein nrdi from aerococcus urinae in oxidized… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6EBQ
Type: protein
Length: 261 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein nrdi
UniProt: A0A178HGH7
Ligands: FMN
Pockets: 4 · best druggability 0.57

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein nrdi	protein	138	37% helix, 22% strand	A0A178HGH7
B	Protein nrdi	protein	123	40% helix, 20% strand	A0A178HGH7

Ligands and binding sites

FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	289	0.57	0.76	26	empty
2	216	0.56	0.79	36	empty
3	72	0.43	0.81	20	FMN
4	65	0.42	0.81	19	FMN

Interfaces

1 interface between chains.

A–B · 737 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6EBQ · Crystal Structure of the Flavoprotein NrdI from Aerococcus urinae in Oxidized Form · the same entry in another collection · 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 A0A178HGH7
Elsewhere: RCSB PDB 6EBQ · PDBe 6EBQ · UniProt A0A178HGH7

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