MolNFT v1 · #137767 · protein
Crystal structure of the plant defensin NSD7 bound to PIP2
5VYP: “Crystal structure of the plant defensin NSD7 bound to PIP2”. X-ray diffraction, 2 ligands (PIO, SO4). MolNFT v1 #137767 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VYP
- Type
- protein
- Length
- 1,145 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- C0HK49
- Ligands
- PIO, SO4
Structure
x-ray diffraction · 4 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, M, N | — | protein | 47 | — | C0HK49 |
| B, C, D, E, F, G, H, I, J, O, P, Q, R, S, T, U, V, W, X | — | protein | 48 | — | C0HK49 |
| K | — | protein | 47 | — | C0HK49 |
| L | — | protein | 45 | — | C0HK49 |
Ligands and binding sites
- PIO · [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2, 3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate · ligand · 24 copies · chains A, B, C, T, V, R, D, E, F, G, H, I, J, K, L, O, Q, S, M, N, P, U, W, X
- SO4 · Sulfate ion · ion · 8 copies · chains A, D, R, G, U
- GOL · Glycerol · additive · 12 copies · chains A, C, I, M, N, P, O, Q, S, U, T, V, G, W, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 5VYP · Crystal structure of the Plant Defensin NsD7 bound to PIP2 · the same entry in another collection · chain J against J, 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 C0HK49
- Elsewhere: RCSB PDB 5VYP · PDBe 5VYP · UniProt C0HK49
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