MolNFT v1 · #144800 · protein
Cross-alpha amyloid-like structure alphaamg
6C4Y: “Cross-alpha amyloid-like structure alphaamg”. X-ray diffraction, 2 ligands (ACE, NH2), 4 pockets (best druggability 0.47). MolNFT v1 #144800 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6C4Y
- Type
- protein
- Length
- 450 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cross-alpha amyloid-like structure alphaamg
- Ligands
- ACE, NH2
- Pockets
- 4 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 92% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, K, I, J, L, M, N, O, P, Q, R | Cross-alpha amyloid-like structure alphaamg | protein | 25 | 92% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 18 copies · chains A, B, C, D, E, F, G, H, K, I, J, L, M, N, O, P, Q, R
- NH2 · Amino group · ion · 18 copies · chains A, B, C, E, D, F, G, I, H, K, M, J, L, N, P, O, Q, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.47 | 0.83 | 18 | empty |
| 2 | 65 | 0.45 | 0.82 | 17 | empty |
| 3 | 77 | 0.44 | 0.80 | 18 | empty |
| 4 | 53 | 0.42 | 0.83 | 17 | empty |
Interfaces
41 interfaces between chains.
- P–R · 650 Ų buried · 3 hydrogen bonds · protein-protein
- L–N · 639 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 636 Ų buried · 3 hydrogen bonds · protein-protein
- E–G · 620 Ų buried · 3 hydrogen bonds · protein-protein
- M–O · 618 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 18 covalent (covalent ligand).
Compared structures
- 6C4Y · Cross-alpha Amyloid-like Structure alphaAmG · 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 6C4Y · PDBe 6C4Y
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