MolNFT v1 · #53681 · protein
Structure of peridinin-chlorophyll-protein reconstituted with chl-D
2X1Z · Peridinin-chlorophyll a-binding protein, chloroplastic: “Structure of peridinin-chlorophyll-protein reconstituted with chl-D”. X-ray diffraction, 6 ligands (PID, CL7, DGD), 2 pockets (best druggability 0.56). MolNFT v1 #53681 on…
- PDB
- 2X1Z
- Type
- protein
- Length
- 151 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peridinin-chlorophyll a-binding protein, chloroplastic
- UniProt
- P80484
- Ligands
- PID, CL7, DGD, CD, NA, CL
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 74% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M | Peridinin-chlorophyll a-binding protein, chloroplastic | protein | 151 | 74% helix, 1% strand | P80484 |
Ligands and binding sites
- PID · Peridinin · ligand · 4 copies · chains M
- CL7 · Chlorophyll D · ligand · chains M
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · chains M
- CD · Cadmium ion · metal · 6 copies · chains M
- NA · Sodium ion · metal · 2 copies · chains M
- CL · Chloride ion · ion · 4 copies · chains M
- PEG · Di(hydroxyethyl)ether · additive · chains M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 372 | 0.56 | 0.73 | 34 | PID, CL7 |
| 2 | 107 | 0.36 | 0.73 | 16 | empty |
Compared structures
- 2X1Z · Structure of Peridinin-Chlorophyll-Protein reconstituted with Chl-d · the same entry in another collection · chain M against M, TM-score 1.00
- P80484 · AlphaFold monomer V2.0 prediction for peridinin-chlorophyll a-binding protein 1… · a predicted model of the same protein · chain M 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 P80484
- Elsewhere: RCSB PDB 2X1Z · PDBe 2X1Z · UniProt P80484
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