Research workbench

Crystal structure of computationally designed armadillo repeat proteins for modular peptide recognition.

Analyse Crystal structure of computationally designed armadillo repeat proteins for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4D49
Type: protein
Length: 988 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Armadillo repeat protein ARM00027; Poly arg decapeptide
Ligands: ARG
Pockets: 3 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 76% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, E, F	Armadillo repeat protein ARM00027	protein	238	79% helix, 0% strand	—
C, D, G, H	Poly arg decapeptide	protein	9	0% helix, 0% strand	—

Ligands and binding sites

ARG · Arginine · ligand · 2 copies · chains D, E

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1174	0.76	0.78	117	empty
2	944	0.75	0.78	88	empty
3	374	0.73	0.84	52	empty

Interfaces

13 interfaces between chains.

B–D · 964 Å² buried · 31 hydrogen bonds · protein-protein
F–H · 961 Å² buried · 32 hydrogen bonds · protein-protein
E–G · 935 Å² buried · 33 hydrogen bonds · protein-protein
A–C · 934 Å² buried · 23 hydrogen bonds · protein-protein
E–F · 504 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

4D49 · Crystal structure of computationally designed armadillo repeat proteins for modular… · the same entry in another collection · chain E against E, 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 4D49 · PDBe 4D49

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