Research workbench
Crystal structure of a multilayer-packed major light-harvesting complex
Analyse Crystal structure of a multilayer-packed major light-harvesting complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LCZ
- Type
- protein
- Length
- 624 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major chlorophyll A/B binding protein LHCB1.3
- UniProt
- B3WFZ6
- Ligands
- CLA, CHL, LUT, NEX, LHG, ZN, NA
- Pockets
- 14 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Major chlorophyll A/B binding protein LHCB1.3 | protein | 208 | 53% helix, 2% strand | B3WFZ6 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 24 copies · chains A, C, B
- CHL · Chlorophyll B · ligand · 18 copies · chains A, B, C
- LUT · (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol · ligand · 6 copies · chains A, B, C
- 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 · 3 copies · chains A, B, C
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 5 copies · chains A, B, C
- NA · Sodium ion · metal · 5 copies · chains B, A, C
- CAC · Cacodylate ion · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 287 | 0.59 | 0.78 | 33 | CLA |
| 2 | 337 | 0.58 | 0.76 | 34 | CHL, CLA |
| 3 | 328 | 0.58 | 0.76 | 36 | CHL, CLA |
| 4 | 306 | 0.57 | 0.76 | 30 | CHL, CLA |
| 5 | 249 | 0.56 | 0.77 | 31 | CLA |
Interfaces
3 interfaces between chains.
- A–B · 483 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 477 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 475 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4LCZ · Crystal structure of a multilayer-packed major light-harvesting complex · the same entry in another collection · chain A 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 B3WFZ6
- Elsewhere: RCSB PDB 4LCZ · PDBe 4LCZ · UniProt B3WFZ6
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