Research workbench

Designed armadillo repeat protein YIII(DQ.V2)4CQI in complex with peptide (KR)4

Analyse Designed armadillo repeat protein YIII(DQ.V2)4CQI in complex with peptide (KR)4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5MFI
Type: protein
Length: 493 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: YIII(DQ.V2)4CQI; (KR)4
Pockets: 3 · best druggability 0.69

Structure

x-ray diffraction · 4 distinct chains · 74% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	YIII(DQ.V2)4CQI	protein	239	79% helix, 0% strand	—
B	YIII(DQ.V2)4CQI	protein	240	74% helix, 0% strand	—
C	(KR)4	protein	8	0% helix, 0% strand	—
D	(KR)4	protein	6	0% helix, 0% strand	—

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	434	0.69	0.80	41	empty
2	278	0.56	0.77	41	empty
3	57	0.28	0.75	15	empty

Interfaces

5 interfaces between chains.

A–C · 741 Å² buried · 29 hydrogen bonds · protein-protein
A–B · 561 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 509 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 296 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 81 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5MFI · Designed armadillo repeat protein YIII(Dq.V2)4CqI in complex with peptide (KR)4 · 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 5MFI · PDBe 5MFI

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