Research workbench
The crystal structure of tumor endothelial marker 8 (TEM8) extracellular domain
Analyse The crystal structure of tumor endothelial marker 8 (TEM8) extracellular domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N2N
- Type
- protein
- Length
- 1,110 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anthrax toxin receptor 1
- UniProt
- Q9H6X2
- Ligands
- MG
- Pockets
- 19 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F, A, B, C, D, E | Anthrax toxin receptor 1 | protein | 185 | 48% helix, 25% strand | Q9H6X2 |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains F, A, B, C, D, E
- ACT · Acetate ion · additive · 18 copies · chains F, A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 771 | 0.68 | 0.75 | 87 | empty |
| 2 | 192 | 0.67 | 0.86 | 29 | empty |
| 3 | 193 | 0.65 | 0.85 | 28 | empty |
| 4 | 181 | 0.65 | 0.85 | 29 | empty |
| 5 | 190 | 0.63 | 0.84 | 31 | empty |
Interfaces
12 interfaces between chains.
- A–D · 598 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 563 Ų buried · 5 hydrogen bonds · protein-protein
- F–C · 554 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 465 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 426 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3N2N · The Crystal Structure of Tumor Endothelial Marker 8 (TEM8) extracellular domain · the same entry in another collection · chain E against E, TM-score 1.00
- Q9H6X2 · AlphaFold monomer V2.0 prediction for anthrax toxin receptor 1 (Q9H6X2) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 Q9H6X2
- Elsewhere: RCSB PDB 3N2N · PDBe 3N2N · UniProt Q9H6X2
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