MolNFT v1 · #126566 · protein

Frutapin complexed with alpha-D-mannose

5M6O: “Frutapin complexed with alpha-D-mannose”. X-ray diffraction, 1 ligand (MAN), 5 pockets (best druggability 0.82). MolNFT v1 #126566 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5M6O
Type: protein
Length: 600 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Frutapin
Ligands: MAN
Pockets: 5 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 0% helix, 66% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Frutapin	protein	150	0% helix, 66% strand	—

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	481	0.82	0.89	62	empty
2	91	0.34	0.74	25	empty
3	81	0.31	0.73	19	empty
4	69	0.29	0.74	18	empty
5	63	0.28	0.74	14	empty

Interfaces

6 interfaces between chains.

A–B · 952 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 929 Å² buried · 17 hydrogen bonds · protein-protein
B–D · 706 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 686 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 51 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5M6O · Frutapin complexed with alpha-D-mannose · 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 5M6O · PDBe 5M6O

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