Research workbench
LH2 complex from marichromatium purpuratum
Analyse LH2 complex from marichromatium purpuratum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZXA
- Type
- protein
- Length
- 791 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lhc domain-containing protein; Light-harvesting protein B:800-850 subunit beta
- UniProt
- W0E6A1, W0E5B0
- Ligands
- BCL, QS2, QSE
- Pockets
- 14 · best druggability 0.76
Structure
electron microscopy · 2 distinct chains · 49% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M | Lhc domain-containing protein | protein | 69 | 33% helix, 0% strand | W0E6A1 |
| B, D, F, H, J, L, N | Light-harvesting protein B:800-850 subunit beta | protein | 44 | 73% helix, 0% strand | W0E5B0 |
Ligands and binding sites
- BCL · Bacteriochlorophyll A · ligand · 21 copies · chains A, B, C, N, M, D, E, F, G, H, I, J, K, L
- QS2 · 9-cis-okenone · ligand · 7 copies · chains A, B, M, N, C, D, E, F, G, H, I, J, K, L
- QSE · all-trans okenone · ligand · 7 copies · chains A, B, C, M, D, E, F, G, H, I, J, K, L, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 908 | 0.76 | 0.78 | 76 | QSE |
| 2 | 1071 | 0.72 | 0.75 | 86 | QSE, BCL |
| 3 | 848 | 0.71 | 0.76 | 68 | QSE, BCL |
| 4 | 564 | 0.67 | 0.77 | 44 | QSE |
| 5 | 577 | 0.67 | 0.76 | 47 | QSE |
Interfaces
35 interfaces between chains.
- A–B · 753 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 749 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 744 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 741 Ų buried · 11 hydrogen bonds · protein-protein
- I–J · 739 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6ZXA · LH2 complex from Marichromatium purpuratum · 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 W0E6A1
- Every structure of UniProt W0E5B0
- Elsewhere: RCSB PDB 6ZXA · PDBe 6ZXA · UniProt W0E6A1 · UniProt W0E5B0
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