MolNFT v1 · #126860 · protein

Designed armadillo repeat protein YIII(DQ.V1)4CPAF in complex with peptide (KR)4

5MFK: “Designed armadillo repeat protein YIII(DQ.V1)4CPAF in complex with peptide (KR)4”. X-ray diffraction, 2 pockets (best druggability 0.70). MolNFT v1 #126860 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5MFK
Type: protein
Length: 488 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: YIII(DQ.V1)4CPAF; (KR)4
Pockets: 2 · best druggability 0.70

Structure

x-ray diffraction · 4 distinct chains · 76% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	YIII(DQ.V1)4CPAF	protein	239	76% helix, 0% strand	—
B	YIII(DQ.V1)4CPAF	protein	240	78% helix, 0% strand	—
C	(KR)4	protein	8	0% helix, 0% strand	—
D	(KR)4	protein	1	0% helix, 0% strand	—

Pockets

2 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	517	0.70	0.80	70	empty
2	96	0.62	0.89	33	empty

Interfaces

4 interfaces between chains.

A–B · 846 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 766 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 326 Å² buried · 1 hydrogen bond · protein-protein
B–D · 122 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5MFK · Designed armadillo repeat protein YIII(Dq.V1)4CPAF 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 5MFK · PDBe 5MFK

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