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
- 7BEE
- Type
- protein
- Length
- 867 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
- 10 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 28% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Collagen-binding protein | protein | 378 | 31% helix, 32% strand | E2RHY7 |
| B | Collagen-binding protein | protein | 373 | 31% helix, 33% strand | E2RHY7 |
| C | 21ER collagen model peptide | protein | 20 | 0% helix, 0% strand | — |
| D, E, G | 21ER collagen model peptide | protein | 19 | 0% helix, 0% strand | — |
| F | 21ER collagen model peptide | protein | 21 | 0% helix, 0% strand | — |
| H | 21ER collagen model peptide | protein | 18 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 6 copies · chains B, C, D, E, A, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1005 | 0.84 | 0.85 | 124 | ACE |
| 2 | 231 | 0.68 | 0.84 | 36 | empty |
| 3 | 75 | 0.54 | 0.85 | 16 | empty |
| 4 | 217 | 0.51 | 0.76 | 22 | empty |
| 5 | 190 | 0.50 | 0.76 | 21 | empty |
Interfaces
18 interfaces between chains.
- A–B · 781 Ų buried · 14 hydrogen bonds · protein-protein
- F–G · 662 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 632 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 619 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 598 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 7BEE · 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 7BEE · PDBe 7BEE · UniProt E2RHY7
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