MolNFT v1 · #105876 · protein
Crystal structure of dccd-modified psbs from spinach
4RI3 · Photosystem II 22 kda protein, chloroplastic: “Crystal structure of dccd-modified psbs from spinach”. X-ray diffraction, 3 ligands (BNG, DCW, HG), 1 pocket (best druggability 0.76). MolNFT v1 #105876 on GenesisL1: 3D structure…
- PDB
- 4RI3
- Type
- protein
- Length
- 336 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, DCW, HG
- Pockets
- 1 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Photosystem II 22 kda protein, chloroplastic | protein | 174 | 59% helix, 6% strand | Q02060 |
| B | Photosystem II 22 kda protein, chloroplastic | protein | 162 | 62% helix, 8% strand | Q02060 |
Ligands and binding sites
- BNG · nonyl beta-D-glucopyranoside · ligand · 4 copies · chains A, B
- DCW · Dicyclohexylurea · ligand · 2 copies · chains A, B
- HG · Mercury (II) ion · metal · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1187 | 0.76 | 0.77 | 71 | DCW |
Interfaces
1 interface between chains.
- A–B · 1697 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4RI3 · Crystal structure of DCCD-modified 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 4RI3 · PDBe 4RI3 · UniProt Q02060
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