MolNFT v1 · #127333 · protein
Crystal structure of an amyloidogenic light chain
5MTL · Light chain DIMER,IGL@ PROTEIN,IGL@ protein: “Crystal structure of an amyloidogenic light chain”. X-ray diffraction, 9 pockets (best druggability 0.61). MolNFT v1 #127333 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MTL
- Type
- protein
- Length
- 798 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain DIMER,IGL@ PROTEIN,IGL@ protein
- UniProt
- Q567P1
- Pockets
- 9 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Light chain DIMER,IGL@ PROTEIN,IGL@ protein | protein | 194 | 7% helix, 47% strand | Q567P1 |
| B | Light chain DIMER,IGL@ PROTEIN,IGL@ protein | protein | 198 | 7% helix, 50% strand | Q567P1 |
| C | Light chain DIMER,IGL@ PROTEIN,IGL@ protein | protein | 206 | 7% helix, 51% strand | Q567P1 |
| D | Light chain DIMER,IGL@ PROTEIN,IGL@ protein | protein | 200 | 7% helix, 50% strand | Q567P1 |
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 536 | 0.61 | 0.74 | 74 | empty |
| 2 | 412 | 0.58 | 0.75 | 53 | empty |
| 3 | 463 | 0.57 | 0.73 | 57 | empty |
| 4 | 111 | 0.40 | 0.76 | 32 | empty |
| 5 | 90 | 0.37 | 0.76 | 22 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1587 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1358 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 439 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 135 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 112 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5MTL · Crystal structure of an amyloidogenic light chain · 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
- Every structure of UniProt Q567P1
- Elsewhere: RCSB PDB 5MTL · PDBe 5MTL · UniProt Q567P1
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