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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: 4AU3
Type: protein
Length: 1,567 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: E2RHY7, Q96A83
Pockets: 20 · best druggability 0.73

Structure

x-ray diffraction · 9 distinct chains · 30% helix, 31% 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, 33% strand	E2RHY7
B	Serpyin peptidase inhibitor, clade H (heat shock protein 47 ), member 1, (collagen binding protein 1)	protein	364	32% helix, 34% strand	E2RHY7
C	Serpin peptidase inhibitor, clade H (heat shock protein 47 ), member 1, (collagen binding protein 1)	protein	370	29% helix, 32% strand	E2RHY7
D	Serpin peptidase inhibitor, clade H (heat shock protein 47 ), member 1, (collagen binding protein 1)	protein	372	31% helix, 33% strand	E2RHY7
E	18ER collagen model peptide 15-R8	protein	15	0% helix, 0% strand	Q96A83
F	18ER collagen model peptide 15-R8	protein	16	0% helix, 0% strand	Q96A83
G, J	18ER collagen model peptide 15-R8	protein	15	0% helix, 0% strand	Q96A83
H	18ER collagen model peptide 15-R8	protein	17	0% helix, 0% strand	Q96A83
I	18ER collagen model peptide 15-R8	protein	16	0% helix, 0% strand	Q96A83

Pockets

20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	719	0.73	0.79	64	empty
2	553	0.71	0.80	43	empty
3	173	0.65	0.85	34	empty
4	140	0.59	0.84	24	empty
5	167	0.59	0.82	33	empty

Interfaces

21 interfaces between chains.

H–I · 541 Å² buried · 6 hydrogen bonds · protein-protein
I–J · 519 Å² buried · 7 hydrogen bonds · protein-protein
E–F · 506 Å² buried · 8 hydrogen bonds · protein-protein
E–G · 502 Å² buried · 7 hydrogen bonds · protein-protein
F–G · 501 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 52 modified (engineered).

Compared structures

4AU3 · Crystal Structure of a Hsp47-collagen complex · the same entry in another collection · chain J against J, TM-score 1.00
Q96A83 · AlphaFold monomer V2.0 prediction for collagen alpha-1(XXVI) chain (Q96A83) · a predicted model of the same protein · chain G against A, TM-score 0.62

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 E2RHY7
Every structure of UniProt Q96A83
Elsewhere: RCSB PDB 4AU3 · PDBe 4AU3 · UniProt E2RHY7 · UniProt Q96A83

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