MolNFT v1 · #126552 · protein
Crystal structure of cardiotoxic bence-jones light chain dimer H9
5M6A: “Crystal structure of cardiotoxic bence-jones light chain dimer H9”. X-ray diffraction, 1 ligand (PO4), 8 pockets (best druggability 0.72). MolNFT v1 #126552 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5M6A
- Type
- protein
- Length
- 852 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bence-jones light chain
- Ligands
- PO4
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bence-jones light chain | protein | 215 | 8% helix, 47% strand | — |
| B | Bence-jones light chain | protein | 214 | 8% helix, 47% strand | — |
| C | Bence-jones light chain | protein | 211 | 8% helix, 50% strand | — |
| D | Bence-jones light chain | protein | 212 | 8% helix, 48% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 3 copies · chains A, C, B, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.72 | 0.76 | 106 | GOL, PO4 |
| 2 | 607 | 0.65 | 0.75 | 86 | empty |
| 3 | 305 | 0.62 | 0.79 | 44 | GOL, PO4 |
| 4 | 501 | 0.61 | 0.75 | 58 | empty |
| 5 | 244 | 0.55 | 0.77 | 41 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1747 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1612 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 420 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 120 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 102 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 5M6A · Crystal structure of cardiotoxic Bence-Jones light chain dimer H9 · 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 5M6A · PDBe 5M6A
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