MolNFT v1 · #80778 · protein
Al-103 Y32F Y96F
3U79 · Amyloidogenic immunoglobulin light chain protein al-103…: “Al-103 Y32F Y96F”. X-ray diffraction, 1 ligand (ZN), 10 pockets (best druggability 0.74). MolNFT v1 #80778 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3U79
- Type
- protein
- Length
- 885 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amyloidogenic immunoglobulin light chain protein al-103 Y32F Y96F, variable domain
- Ligands
- ZN
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, F, H | Amyloidogenic immunoglobulin light chain protein al-103 Y32F Y96F, variable domain | protein | 111 | 3% helix, 47% strand | — |
| D, E, G | Amyloidogenic immunoglobulin light chain protein al-103 Y32F Y96F, variable domain | protein | 110 | 3% helix, 46% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 16 copies · chains A, G, F, B, C, D, E, H
- ACT · Acetate ion · additive · 9 copies · chains A, G, B, C, D, E, F
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 711 | 0.74 | 0.80 | 66 | ACT |
| 2 | 598 | 0.73 | 0.81 | 80 | ACT |
| 3 | 303 | 0.63 | 0.80 | 44 | empty |
| 4 | 251 | 0.54 | 0.76 | 41 | empty |
| 5 | 153 | 0.47 | 0.77 | 30 | ACT |
Interfaces
13 interfaces between chains.
- C–G · 716 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 712 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 685 Ų buried · 8 hydrogen bonds · protein-protein
- D–H · 677 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 352 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3U79 · Al-103 Y32F Y96F · 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 3U79 · PDBe 3U79
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