MolNFT v1 · #114053 · protein

Structure of MOEN5-SSO7D fusion protein in complex with beta-nonyl glucoside

5B0L · MOEN5,DNA-binding protein 7D: “Structure of MOEN5-SSO7D fusion protein in complex with beta-nonyl glucoside”. X-ray diffraction, 1 ligand (BNG), 20 pockets (best druggability 0.86). MolNFT v1 #114053 on GenesisL1: 3D structure…

PDB: 5B0L
Type: protein
Length: 2,393 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MOEN5,DNA-binding protein 7D
UniProt: A0A010, P39476
Ligands: BNG
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 8 distinct chains · 70% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MOEN5,DNA-binding protein 7D	protein	264	77% helix, 0% strand	A0A010, P39476
B	MOEN5,DNA-binding protein 7D	protein	334	64% helix, 9% strand	A0A010, P39476
C	MOEN5,DNA-binding protein 7D	protein	265	75% helix, 0% strand	A0A010, P39476
D	MOEN5,DNA-binding protein 7D	protein	333	63% helix, 9% strand	A0A010, P39476
E	MOEN5,DNA-binding protein 7D	protein	269	76% helix, 0% strand	A0A010, P39476
F	MOEN5,DNA-binding protein 7D	protein	332	66% helix, 9% strand	A0A010, P39476
G	MOEN5,DNA-binding protein 7D	protein	263	79% helix, 0% strand	A0A010, P39476
H	MOEN5,DNA-binding protein 7D	protein	333	66% helix, 10% strand	A0A010, P39476

Ligands and binding sites

BNG · nonyl beta-D-glucopyranoside · ligand · 13 copies · chains A, E, B, H, C, G, D, F

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	613	0.86	0.91	85	BNG
2	476	0.85	0.91	62	BNG
3	526	0.85	0.91	72	BNG
4	463	0.83	0.90	63	BNG
5	779	0.81	0.84	70	BNG

Interfaces

14 interfaces between chains.

E–F · 1862 Å² buried · 23 hydrogen bonds · protein-protein
G–H · 1854 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 1803 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1787 Å² buried · 16 hydrogen bonds · protein-protein
D–F · 999 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

5B0L · Structure of MoeN5-Sso7d fusion protein in complex with beta-nonyl glucoside · the same entry in another collection · chain A against A, TM-score 1.00
P39476 · AlphaFold monomer V2.0 prediction for DNA-binding protein 7D (P39476) · a predicted model of the same protein · chain F against A, TM-score 0.19

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 A0A010
Every structure of UniProt P39476
Elsewhere: RCSB PDB 5B0L · PDBe 5B0L · UniProt A0A010 · UniProt P39476

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