Research workbench
X-ray crystallographic structure of a covalent trimer derived from a- beta 17_36. synchrotron data set. (ORN)CVF(MEA)CED(ORN)AIIGL(ORN)V.
Analyse X-ray crystallographic structure of a covalent trimer derived from a- beta… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SUR
- Type
- protein
- Length
- 64 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16MER a-beta peptide: orn-cys-val-phe-mea-cys-glu-asp-orn- ala-ile-ile-gly-leu-orn-val
- Ligands
- NA, CL
- Pockets
- 1 · best druggability 0.28
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 63% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 16MER a-beta peptide: orn-cys-val-phe-mea-cys-glu-asp-orn- ala-ile-ile-gly-leu-orn-val | protein | 16 | 0% helix, 63% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B, D
- CL · Chloride ion · ion · 2 copies · chains C, D
- HEZ · Hexane-1,6-diol · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.28 | 0.74 | 14 | empty |
Interfaces
4 interfaces between chains.
- A–B · 233 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 197 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 186 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 185 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (nonstandard).
Compared structures
- 5SUR · X-ray crystallographic structure of a covalent trimer derived from A-beta 17_36.… · 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
- Elsewhere: RCSB PDB 5SUR · PDBe 5SUR
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