Research workbench

Single-particle reconstruction of DARP14 - a designed protein scaffold displaying ~17KDA darpin proteins - scaffold

Analyse Single-particle reconstruction of DARP14 - a designed protein scaffold… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6C9I
Type: protein
Length: 3,087 residues
Chains: 24
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DARP14 - subunit a with darpin; DARP14 - subunit B
UniProt: O58404, Q9I2D8
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 6 distinct chains · 62% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, I, Q	DARP14 - subunit a with darpin	protein	140	76% helix, 0% strand	O58404
B, J, R	DARP14 - subunit a with darpin	protein	139	77% helix, 0% strand	O58404
C, K, S	DARP14 - subunit a with darpin	protein	138	78% helix, 0% strand	O58404
D, L, T	DARP14 - subunit a with darpin	protein	141	76% helix, 0% strand	O58404
E, F, G, M, N, O, U, V, W	DARP14 - subunit B	protein	118	28% helix, 38% strand	Q9I2D8
H, P, X	DARP14 - subunit B	protein	117	27% helix, 38% strand	Q9I2D8

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	642	0.83	0.87	51	empty
2	655	0.82	0.87	54	empty
3	673	0.82	0.86	54	empty
4	664	0.82	0.87	51	empty
5	880	0.75	0.79	118	empty

Interfaces

63 interfaces between chains.

E–M · 1261 Å² buried · 32 hydrogen bonds · protein-protein
G–P · 1260 Å² buried · 32 hydrogen bonds · protein-protein
E–U · 1259 Å² buried · 32 hydrogen bonds · protein-protein
M–U · 1258 Å² buried · 32 hydrogen bonds · protein-protein
O–X · 1258 Å² buried · 33 hydrogen bonds · protein-protein

Compared structures

6C9I · Single-Particle reconstruction of DARP14 - A designed protein scaffold displaying ~17kDa… · the same entry in another collection · chain F against F, 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
Every structure of UniProt O58404
Every structure of UniProt Q9I2D8
Elsewhere: RCSB PDB 6C9I · PDBe 6C9I · UniProt O58404 · UniProt Q9I2D8

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.