MolNFT v1 · #124608 · protein
Crystal structure of the plant defensin NSD7 bound to phosphatidic acid
5KK4: “Crystal structure of the plant defensin NSD7 bound to phosphatidic acid”. X-ray diffraction, 2 ligands (44E, SO4), 2 pockets (best druggability 0.36). MolNFT v1 #124608 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KK4
- Type
- protein
- Length
- 284 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NSD7
- Ligands
- 44E, SO4
- Pockets
- 2 · best druggability 0.36
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | NSD7 | protein | 47 | 21% helix, 28% strand | — |
| E, F | NSD7 | protein | 48 | 21% helix, 27% strand | — |
Ligands and binding sites
- 44E · (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate · ligand · 6 copies · chains B, C, D, E, F
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D, E
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, B, C, D, E, F
- ACT · Acetate ion · additive · 3 copies · chains A, B, C
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 | 105 | 0.36 | 0.73 | 15 | empty |
| 2 | 91 | 0.34 | 0.73 | 15 | empty |
Interfaces
5 interfaces between chains.
- C–D · 442 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 408 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 390 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 257 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 250 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 5KK4 · Crystal Structure of the Plant Defensin NsD7 bound to Phosphatidic Acid · 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 5KK4 · PDBe 5KK4
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