MolNFT v1 · #184747 · protein
Structure of caspase-3 cleaved RXKR9 in complex with a sybody at 4.3A
7P16 · Xk-related protein: “Structure of caspase-3 cleaved RXKR9 in complex with a sybody at 4.3A”. Electron microscopy, 1 ligand (PLC), 7 pockets (best druggability 0.72). MolNFT v1 #184747 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7P16
- Type
- protein
- Length
- 444 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xk-related protein; Sybody
- UniProt
- Q5GH54
- Ligands
- PLC
- Pockets
- 7 · best druggability 0.72
Structure
electron microscopy · 2 distinct chains · 61% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xk-related protein | protein | 318 | 83% helix, 0% strand | Q5GH54 |
| B | Sybody | protein | 126 | 5% helix, 44% strand | — |
Ligands and binding sites
- PLC · Diundecyl phosphatidyl choline · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 208 | 0.72 | 0.88 | 28 | empty |
| 2 | 421 | 0.69 | 0.81 | 46 | empty |
| 3 | 301 | 0.60 | 0.77 | 32 | PLC |
| 4 | 52 | 0.58 | 0.91 | 21 | empty |
| 5 | 162 | 0.57 | 0.81 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 723 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7P16 · Structure of caspase-3 cleaved rXKR9 in complex with a sybody at 4.3A · 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 Q5GH54
- Elsewhere: RCSB PDB 7P16 · PDBe 7P16 · UniProt Q5GH54
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