MolNFT v1 · #84037 · protein

Crystal structure of FMN-bound dszc from rhodococcus erythropolis D-1

3X0Y: “Crystal structure of FMN-bound dszc from rhodococcus erythropolis D-1”. X-ray diffraction, 1 ligand (FMN), 20 pockets (best druggability 0.88). MolNFT v1 #84037 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3X0Y
Type: protein
Length: 3,206 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dszc
Ligands: FMN
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 3 distinct chains · 57% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Dszc	protein	402	57% helix, 10% strand	—
B, C, F, H	Dszc	protein	400	57% helix, 11% strand	—
E, G	Dszc	protein	401	58% helix, 10% strand	—

Ligands and binding sites

FMN · Flavin mononucleotide · ligand · 4 copies · chains A, F, C, E, B, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1083	0.88	0.90	146	FMN
2	477	0.86	0.92	82	empty
3	467	0.85	0.92	72	FMN
4	483	0.85	0.92	69	FMN
5	560	0.84	0.90	84	empty

Interfaces

21 interfaces between chains.

A–F · 2142 Å² buried · 16 hydrogen bonds · protein-protein
B–D · 2109 Å² buried · 17 hydrogen bonds · protein-protein
C–E · 2084 Å² buried · 14 hydrogen bonds · protein-protein
G–H · 2052 Å² buried · 16 hydrogen bonds · protein-protein
D–E · 1524 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

3X0Y · Crystal structure of FMN-bound DszC from Rhodococcus erythropolis D-1 · 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
Elsewhere: RCSB PDB 3X0Y · PDBe 3X0Y

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