MolNFT v1 · #114871 · protein

The de novo evolutionary emergence of a symmetrical protein is shaped by folding constraints

5C2N · Beta propeller: “The de novo evolutionary emergence of a symmetrical protein is shaped by folding constraints”. X-ray diffraction, 1 ligand (NAG), 6 pockets (best druggability 0.78). MolNFT v1 #114871 on GenesisL1: 3D structure…

PDB: 5C2N
Type: protein
Length: 700 residues
Chains: 15
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta propeller
Ligands: NAG
Pockets: 6 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, G, J, O	Beta propeller	protein	46	9% helix, 43% strand	—
B, C, E, F, H, I, K, L, M, N	Beta propeller	protein	47	9% helix, 43% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, C, B, D, G, H, E, I, O, F, J, K, L, N, M

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

Pockets

6 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	444	0.78	0.86	35	empty
2	460	0.78	0.85	35	empty
3	452	0.77	0.85	36	empty
4	269	0.63	0.81	39	NAG
5	321	0.62	0.79	48	NAG

Interfaces

23 interfaces between chains.

F–H · 665 Å² buried · 2 hydrogen bonds · protein-protein
E–I · 652 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 648 Å² buried · 5 hydrogen bonds · protein-protein
M–O · 641 Å² buried · 3 hydrogen bonds · protein-protein
F–J · 641 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5C2N · The de novo evolutionary emergence of a symmetrical protein is shaped by folding… · 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 5C2N · PDBe 5C2N

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