MolNFT v1 · #61198 · protein
C-terminal domain of probable hemolysin from chromobacterium violaceum
3DED: “C-terminal domain of probable hemolysin from chromobacterium violaceum”. X-ray diffraction, 1 ligand (CA), 4 pockets (best druggability 0.56). MolNFT v1 #61198 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3DED
- Type
- protein
- Length
- 523 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable hemolysin
- UniProt
- Q7P1I2
- Ligands
- CA
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Probable hemolysin | protein | 87 | 22% helix, 36% strand | Q7P1I2 |
| B, D, F | Probable hemolysin | protein | 86 | 23% helix, 36% strand | Q7P1I2 |
| C | Probable hemolysin | protein | 91 | 18% helix, 34% strand | Q7P1I2 |
Ligands and binding sites
- CA · Calcium ion · metal · 9 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 168 | 0.56 | 0.80 | 25 | empty |
| 2 | 79 | 0.36 | 0.76 | 24 | empty |
| 3 | 74 | 0.32 | 0.74 | 17 | empty |
| 4 | 61 | 0.31 | 0.76 | 23 | empty |
Interfaces
5 interfaces between chains.
- C–D · 646 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 638 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 619 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 302 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 287 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 3DED · C-terminal domain of Probable hemolysin from Chromobacterium violaceum · 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 Q7P1I2
- Elsewhere: RCSB PDB 3DED · PDBe 3DED · UniProt Q7P1I2
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