Research workbench
Crystal structure of the orphan region of human ENDOGLIN/CD105
Analyse Crystal structure of the orphan region of human ENDOGLIN/CD105 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I04
- Type
- protein
- Length
- 668 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose-binding periplasmic PROTEIN,ENDOGLIN
- UniProt
- P0AEX9, P17813
- Ligands
- GLC, NAG
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltose-binding periplasmic PROTEIN,ENDOGLIN | protein | 668 | 28% helix, 33% strand | P0AEX9, P17813 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- PGE · Triethylene glycol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 295 | 0.70 | 0.84 | 32 | GLC |
| 2 | 424 | 0.69 | 0.80 | 52 | empty |
| 3 | 330 | 0.61 | 0.78 | 32 | empty |
| 4 | 82 | 0.45 | 0.81 | 15 | empty |
| 5 | 81 | 0.42 | 0.80 | 25 | empty |
Modifications
Observed in the structure: 2 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
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
- Elsewhere: RCSB PDB 5I04 · PDBe 5I04 · UniProt P0AEX9 · UniProt P17813
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