MolNFT v1 · #114054 · protein

Structure of MOEN5-SSO7D fusion protein in complex with beta-dodecyl maltoside

5B0M · MOEN5,DNA-binding protein 7D: “Structure of MOEN5-SSO7D fusion protein in complex with beta-dodecyl maltoside”. X-ray diffraction, 19 pockets (best druggability 0.86). MolNFT v1 #114054 on GenesisL1: 3D structure, binding sites and…

PDB: 5B0M
Type: protein
Length: 2,396 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MOEN5,DNA-binding protein 7D
UniProt: A0A010, P39476
Pockets: 19 · best druggability 0.86

Structure

x-ray diffraction · 7 distinct chains · 69% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	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
D	MOEN5,DNA-binding protein 7D	protein	332	63% helix, 10% strand	A0A010, P39476
E	MOEN5,DNA-binding protein 7D	protein	270	75% helix, 0% strand	A0A010, P39476
F	MOEN5,DNA-binding protein 7D	protein	332	63% helix, 11% strand	A0A010, P39476
G	MOEN5,DNA-binding protein 7D	protein	267	76% helix, 0% strand	A0A010, P39476
H	MOEN5,DNA-binding protein 7D	protein	333	66% helix, 10% strand	A0A010, P39476

Ligands and binding sites

LMT · Dodecyl-beta-D-maltoside · additive · 8 copies · chains E, F, G, H, C, B

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

Pockets

19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	799	0.86	0.89	92	empty
2	664	0.85	0.89	73	empty
3	510	0.84	0.91	79	empty
4	444	0.83	0.90	61	empty
5	715	0.81	0.85	72	LMT

Interfaces

14 interfaces between chains.

E–F · 1848 Å² buried · 24 hydrogen bonds · protein-protein
G–H · 1839 Å² buried · 28 hydrogen bonds · protein-protein
A–B · 1836 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 1818 Å² buried · 17 hydrogen bonds · protein-protein
A–E · 942 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5B0M · Structure of MoeN5-Sso7d fusion protein in complex with beta-dodecyl maltoside · 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 5B0M · PDBe 5B0M · UniProt A0A010 · UniProt P39476

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