Research workbench
Crystal structure of macrocycles containing ABETA17-23 (LVF(MEA)AED) and ABETA30-36 (AIIGL(ORN)V)
Analyse Crystal structure of macrocycles containing ABETA17-23 (LVF(MEA)AED) and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NW9
- Type
- protein
- Length
- 192 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclic hexadecapeptide (ORN)LVF(MEA)AED(ORN)AIIGL(ORN)V
- Ligands
- NA, CL
- Pockets
- 1 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 63% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Cyclic hexadecapeptide (ORN)LVF(MEA)AED(ORN)AIIGL(ORN)V | protein | 16 | 0% helix, 63% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains D, L, K
- CL · Chloride ion · ion · 3 copies · chains C, K, B, G, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 835 | 0.67 | 0.73 | 69 | empty |
Interfaces
33 interfaces between chains.
- G–I · 247 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 247 Ų buried · 3 hydrogen bonds · protein-protein
- J–L · 243 Ų buried · 2 hydrogen bonds · protein-protein
- D–E · 243 Ų buried · 2 hydrogen bonds · protein-protein
- K–L · 241 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified (nonstandard).
Compared structures
- 4NW9 · Crystal structure of macrocycles containing Abeta17-23 (LVF(MEA)AED) and Abeta30-36… · 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 4NW9 · PDBe 4NW9
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