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Crystal structure of reduced yqjm from bacillus subtilis

Analyse Crystal structure of reduced yqjm from bacillus subtilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1Z48
Type: protein
Length: 674 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable NADH-dependent flavin oxidoreductase yqjm
EC: 1.-.-.-
UniProt: P54550
Ligands: FMN
Pockets: 4 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Probable NADH-dependent flavin oxidoreductase yqjm (EC 1.-.-.-)	protein	337	38% helix, 16% strand	P54550

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	464	0.69	0.80	54	FMN
2	447	0.66	0.79	47	FMN
3	202	0.49	0.75	32	empty
4	66	0.29	0.74	10	empty

Interfaces

1 interface between chains.

A–B · 1129 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 modified (engineered).

Compared structures

1Z48 · Crystal structure of reduced YqjM from Bacillus subtilis · the same entry in another collection · chain A against A, TM-score 1.00
P54550 · AlphaFold monomer V2.0 prediction for NADPH dehydrogenase (P54550) · a predicted model of the same protein · 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 P54550
Elsewhere: RCSB PDB 1Z48 · PDBe 1Z48 · UniProt P54550

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