Research workbench
Crystal structure of spinach major light-harvesting complex at 2.72 ångström resolution
Analyse Crystal structure of spinach major light-harvesting complex at 2.72 ångström… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RWT
- Type
- protein
- Length
- 2,181 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chlorophyll a-B binding protein, chloroplast
- UniProt
- P12333
- Ligands
- CLA, CHL, LUT, BNG, XAT, NEX, LHG, DGD, NA
- Pockets
- 20 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, G, H, I, J | Chlorophyll a-B binding protein, chloroplast | protein | 218 | 54% helix, 2% strand | P12333 |
| F | Chlorophyll a-B binding protein, chloroplast | protein | 219 | 53% helix, 2% strand | P12333 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 80 copies · chains A, B, F, G, C, H, E, D, I, J
- CHL · Chlorophyll B · ligand · 60 copies · chains A, J, B, G, F, C, E, H, D, I
- LUT · (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol · ligand · 20 copies · chains A, B, C, D, E, F, G, H, I, J
- BNG · nonyl beta-D-glucopyranoside · ligand · 10 copies
- XAT · (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-tetrahydro-beta,beta-carotene-3,3'-diol · ligand · 10 copies · chains A, B, G, F, C, H, D, I, E, J
- NEX · (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R, 6R)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13, 15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 10 copies · chains A, I, J, B, F, C, G, H, D, E
- NA · Sodium ion · metal
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 490 | 0.67 | 0.78 | 53 | CLA |
| 2 | 427 | 0.65 | 0.78 | 54 | CLA |
| 3 | 302 | 0.58 | 0.77 | 32 | CHL, CLA |
| 4 | 301 | 0.58 | 0.77 | 33 | CHL, CLA |
| 5 | 276 | 0.58 | 0.78 | 36 | CLA |
Interfaces
14 interfaces between chains.
- B–F · 784 Ų buried · 1 hydrogen bond · protein-protein
- F–G · 773 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 771 Ų buried · 1 hydrogen bond · protein-protein
- C–H · 771 Ų buried · 3 hydrogen bonds · protein-protein
- D–I · 759 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1RWT · Crystal Structure of Spinach Major Light-harvesting complex at 2.72 Angstrom Resolution · the same entry in another collection · chain J against J, TM-score 1.00
- P12333 · AlphaFold monomer V2.0 prediction for chlorophyll a-B binding protein, chloroplastic… · a predicted model of the same protein · chain I 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 P12333
- Elsewhere: RCSB PDB 1RWT · PDBe 1RWT · UniProt P12333
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