MolNFT v1 · #105875 · protein
Crystal structure of the photoprotective protein psbs from spinach
4RI2 · Photosystem II 22 kda protein, chloroplastic: “Crystal structure of the photoprotective protein psbs from spinach”. X-ray diffraction, 3 ligands (BNG, CLA, HG), 2 pockets (best druggability 0.76). MolNFT v1 #105875 on GenesisL1: 3D…
- PDB
- 4RI2
- Type
- protein
- Length
- 340 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosystem II 22 kda protein, chloroplastic
- UniProt
- Q02060
- Ligands
- BNG, CLA, HG
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Photosystem II 22 kda protein, chloroplastic | protein | 177 | 56% helix, 7% strand | Q02060 |
| B | Photosystem II 22 kda protein, chloroplastic | protein | 163 | 61% helix, 8% strand | Q02060 |
Ligands and binding sites
- BNG · nonyl beta-D-glucopyranoside · ligand · 4 copies · chains A, B
- CLA · Chlorophyll A · ligand · chains A, B
- HG · Mercury (II) ion · metal · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 965 | 0.76 | 0.78 | 66 | empty |
| 2 | 94 | 0.63 | 0.90 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 1719 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4RI2 · Crystal structure of the photoprotective protein PsbS from spinach · the same entry in another collection · chain A against A, TM-score 1.00
- Q02060 · AlphaFold monomer V2.0 prediction for photosystem II 22 kda protein, chloroplastic… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q02060
- Elsewhere: RCSB PDB 4RI2 · PDBe 4RI2 · UniProt Q02060
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