Research workbench

Crystal structure of a HSP47-collagen complex

Analyse Crystal structure of a HSP47-collagen complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4AU2
Type: protein
Length: 1,499 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding…
UniProt: C7C419
Ligands: ACE
Pockets: 20 · best druggability 0.68

Structure

x-ray diffraction · 7 distinct chains · 31% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)	protein	367	32% helix, 32% strand	C7C419
B	Serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)	protein	354	31% helix, 34% strand	C7C419
C	Serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)	protein	338	32% helix, 34% strand	C7C419
D	Serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)	protein	359	31% helix, 34% strand	C7C419
E, F, H, I	15ER collagen model peptide 15-R8	protein	14	0% helix, 0% strand	—
G	15ER collagen model peptide 15-R8	protein	13	0% helix, 0% strand	—
J	15ER collagen model peptide 15-R8	protein	12	0% helix, 0% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 4 copies · chains D, E, F, G, B, H, I, J

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

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	523	0.68	0.79	44	empty
2	380	0.63	0.78	32	empty
3	258	0.61	0.80	28	empty
4	343	0.61	0.78	52	empty
5	197	0.55	0.79	29	empty

Interfaces

27 interfaces between chains.

B–D · 581 Å² buried · 10 hydrogen bonds · protein-protein
F–G · 463 Å² buried · 6 hydrogen bonds · protein-protein
H–I · 460 Å² buried · 6 hydrogen bonds · protein-protein
E–F · 458 Å² buried · 6 hydrogen bonds · protein-protein
I–J · 427 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

4AU2 · Crystal Structure of a Hsp47-collagen complex · 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
Every structure of UniProt C7C419
Elsewhere: RCSB PDB 4AU2 · PDBe 4AU2 · UniProt C7C419

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