MolNFT v1 · #120856 · protein

Structure of B. megaterium NFRA1

5HDJ: “Structure of B. megaterium NFRA1”. X-ray diffraction, 1 ligand (FMN), 6 pockets (best druggability 0.67). MolNFT v1 #120856 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5HDJ
Type: protein
Length: 495 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NFRA1
UniProt: A0A0K0VJM9
Ligands: FMN
Pockets: 6 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 52% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NFRA1	protein	247	53% helix, 14% strand	A0A0K0VJM9
B	NFRA1	protein	248	52% helix, 14% strand	A0A0K0VJM9

Ligands and binding sites

FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 3 copies · chains A, B

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

Pockets

6 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	403	0.67	0.80	44	FMN
2	399	0.65	0.79	44	FMN, EDO
3	67	0.34	0.76	16	empty
4	71	0.31	0.74	14	empty
5	58	0.30	0.76	15	empty

Interfaces

1 interface between chains.

A–B · 5251 Å² buried · 75 hydrogen bonds · protein-protein

Compared structures

5HDJ · Structure of B. megaterium NfrA1 · 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 A0A0K0VJM9
Elsewhere: RCSB PDB 5HDJ · PDBe 5HDJ · UniProt A0A0K0VJM9

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