Research workbench
Crystal structure of the orphan region of human ENDOGLIN/CD105 in complex with BMP9
Analyse Crystal structure of the orphan region of human ENDOGLIN/CD105 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HZW
- Type
- protein
- Length
- 773 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose-binding periplasmic PROTEIN,ENDOGLIN; GROWTH/DIFFERENTIATION factor 2
- UniProt
- P0AEX9, P17813, Q9UK05
- Ligands
- GLC, NAG
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltose-binding periplasmic PROTEIN,ENDOGLIN | protein | 668 | 28% helix, 33% strand | P0AEX9, P17813 |
| B | GROWTH/DIFFERENTIATION factor 2 | protein | 105 | 11% helix, 46% strand | Q9UK05 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 651 | 0.80 | 0.85 | 54 | GLC |
| 2 | 489 | 0.73 | 0.82 | 71 | NAG |
| 3 | 186 | 0.52 | 0.78 | 21 | empty |
| 4 | 60 | 0.48 | 0.84 | 18 | empty |
| 5 | 102 | 0.46 | 0.80 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 687 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5HZW · Crystal structure of the orphan region of human endoglin/CD105 in complex with BMP9 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UK05 · AlphaFold monomer V2.0 prediction for GROWTH/DIFFERENTIATION factor 2 (Q9UK05) · a predicted model of the same protein · chain B against A, TM-score 0.90
- P17813 · AlphaFold monomer V2.0 prediction for endoglin (P17813) · a predicted model of the same protein · chain A against A, TM-score 0.46
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 P0AEX9
- Every structure of UniProt P17813
- Every structure of UniProt Q9UK05
- Elsewhere: RCSB PDB 5HZW · PDBe 5HZW · UniProt P0AEX9 · UniProt P17813 · UniProt Q9UK05
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