Research workbench
Crystal structure of toxin MT9 from mamba venom
Analyse Crystal structure of toxin MT9 from mamba venom in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R5M
- Type
- protein
- Length
- 171 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dendroaspis polylepis MT9
- Ligands
- ACE, SO4
- Pockets
- 2 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Dendroaspis polylepis MT9 | protein | 57 | 0% helix, 49% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains C
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C
- PGO · S-1,2-propanediol · additive · 2 copies · chains A
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 173 | 0.50 | 0.77 | 29 | SO4 |
| 2 | 56 | 0.34 | 0.78 | 18 | SO4 |
Interfaces
3 interfaces between chains.
- A–B · 369 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 337 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 307 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6R5M · Crystal structure of toxin MT9 from mamba venom · 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 6R5M · PDBe 6R5M
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