Research workbench
Crystal structure of a HSP47-collagen peptide complex
Analyse Crystal structure of a HSP47-collagen peptide complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BDU
- Type
- protein
- Length
- 868 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Collagen-binding protein; 21ER collagen model peptide
- UniProt
- E2RHY7
- Ligands
- ACE
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 29% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Collagen-binding protein | protein | 374 | 32% helix, 33% strand | E2RHY7 |
| B | Collagen-binding protein | protein | 371 | 32% helix, 33% strand | E2RHY7 |
| C | 21ER collagen model peptide | protein | 20 | 0% helix, 0% strand | — |
| D, F, G | 21ER collagen model peptide | protein | 21 | 0% helix, 0% strand | — |
| E, H | 21ER collagen model peptide | protein | 20 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 696 | 0.81 | 0.85 | 86 | ACE |
| 2 | 513 | 0.78 | 0.86 | 57 | ACE |
| 3 | 122 | 0.65 | 0.88 | 32 | empty |
| 4 | 169 | 0.46 | 0.76 | 23 | empty |
| 5 | 156 | 0.46 | 0.76 | 24 | empty |
Interfaces
19 interfaces between chains.
- A–B · 695 Ų buried · 12 hydrogen bonds · protein-protein
- F–G · 655 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 654 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 637 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 636 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7BDU · Crystal structure of a Hsp47-collagen peptide 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 E2RHY7
- Elsewhere: RCSB PDB 7BDU · PDBe 7BDU · UniProt E2RHY7
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