MolNFT v1 · #40434 · protein

Blub bound to oxidized FMN

2ISJ: “Blub bound to oxidized FMN”. X-ray diffraction, 1 ligand (FMN), 20 pockets (best druggability 0.83). MolNFT v1 #40434 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2ISJ
Type: protein
Length: 1,752 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Blub
UniProt: Q92PC8
Ligands: FMN
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Blub	protein	219	40% helix, 18% strand	Q92PC8

Ligands and binding sites

FMN · Flavin mononucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	175	0.83	0.98	28	FMN
2	181	0.83	0.98	31	FMN
3	182	0.83	0.97	34	FMN
4	171	0.83	0.97	29	FMN
5	169	0.82	0.97	28	FMN

Interfaces

14 interfaces between chains.

G–H · 5067 Å² buried · 74 hydrogen bonds · protein-protein
E–F · 5026 Å² buried · 70 hydrogen bonds · protein-protein
C–D · 5022 Å² buried · 77 hydrogen bonds · protein-protein
A–B · 5020 Å² buried · 74 hydrogen bonds · protein-protein
A–D · 362 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

2ISJ · BluB bound to oxidized FMN · the same entry in another collection · chain H against H, TM-score 1.00
Q92PC8 · AlphaFold monomer V2.0 prediction for 5,6-dimethylbenzimidazole synthase (Q92PC8) · a predicted model of the same protein · chain D 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 Q92PC8
Elsewhere: RCSB PDB 2ISJ · PDBe 2ISJ · UniProt Q92PC8

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