MolNFT v1 · #120334 · protein

Structure of MOEN5-SSO7D fusion protein in complex with a permethylated substrate analogue

5GWW · MOEN5,DNA-binding protein 7D: “Structure of MOEN5-SSO7D fusion protein in complex with a permethylated substrate analogue”. X-ray diffraction, 1 ligand (7B5), 7 pockets (best druggability 0.82). MolNFT v1 #120334 on GenesisL1: 3D…

PDB: 5GWW
Type: protein
Length: 1,191 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MOEN5,DNA-binding protein 7D
UniProt: A0A010, P39476
Ligands: 7B5
Pockets: 7 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 71% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MOEN5,DNA-binding protein 7D	protein	264	78% helix, 0% strand	A0A010, P39476
B	MOEN5,DNA-binding protein 7D	protein	332	67% helix, 10% strand	A0A010, P39476
C	MOEN5,DNA-binding protein 7D	protein	262	78% helix, 0% strand	A0A010, P39476
D	MOEN5,DNA-binding protein 7D	protein	333	65% helix, 9% strand	A0A010, P39476

Ligands and binding sites

7B5 · methyl (2R)-3-dimethoxyphosphoryloxy-2-[(2Z,6E)-3,7,11-trimethyldodeca-2,6,10-trienoxy]propanoate · ligand · chains C, D

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

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	931	0.82	0.83	80	empty
2	1120	0.79	0.80	75	empty
3	698	0.78	0.83	65	empty
4	648	0.75	0.81	45	7B5
5	297	0.57	0.77	50	empty

Interfaces

4 interfaces between chains.

C–D · 1854 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 1844 Å² buried · 24 hydrogen bonds · protein-protein
A–C · 828 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 323 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5GWW · Structure of MoeN5-Sso7d fusion protein in complex with a permethylated substrate analogue · the same entry in another collection · chain D against D, TM-score 1.00
P39476 · AlphaFold monomer V2.0 prediction for DNA-binding protein 7D (P39476) · a predicted model of the same protein · chain D 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 5GWW · PDBe 5GWW · UniProt A0A010 · UniProt P39476

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