Research workbench
Crystallographic structure of the LH3 complex from rhodopseudomonas acidophila strain 7050
Analyse Crystallographic structure of the LH3 complex from rhodopseudomonas acidophila… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IJD
- Type
- protein
- Length
- 258 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light-harvesting protein B-800/820, alpha chain; Light-harvesting protein B-800/820, beta…
- UniProt
- P35089, P35094
- Ligands
- BCL, RPA
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Light-harvesting protein B-800/820, alpha chain | protein | 46 | 76% helix, 0% strand | P35089 |
| B, D, F | Light-harvesting protein B-800/820, beta chain | protein | 40 | 78% helix, 0% strand | P35094 |
Ligands and binding sites
- BCL · Bacteriochlorophyll A · ligand · 9 copies · chains A, B, C, D, E, F
- RPA · Rhodopinal glucoside · ligand · 3 copies · chains A, B, C, D, E, F
- BOG · octyl beta-D-glucopyranoside · additive · 3 copies · chains B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 414 | 0.61 | 0.76 | 46 | RPA |
| 2 | 435 | 0.61 | 0.75 | 43 | RPA |
| 3 | 262 | 0.53 | 0.75 | 26 | empty |
| 4 | 179 | 0.45 | 0.74 | 18 | empty |
| 5 | 78 | 0.34 | 0.75 | 13 | empty |
Interfaces
9 interfaces between chains.
- A–B · 680 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 679 Ų buried · 1 hydrogen bond · protein-protein
- E–F · 676 Ų buried · 1 hydrogen bond · protein-protein
- C–E · 495 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 492 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (formylation).
Compared structures
- 1IJD · Crystallographic Structure of the LH3 Complex from Rhodopseudomonas acidophila strain 7050 · the same entry in another collection · chain F against F, TM-score 1.00
- P35089 · AlphaFold monomer V2.0 prediction for light-harvesting protein B-800/820 alpha chain… · a predicted model of the same protein · chain A against A, TM-score 0.94
- P35094 · AlphaFold monomer V2.0 prediction for light-harvesting protein B-800/820 beta chain… · a predicted model of the same protein · chain B against A, TM-score 0.86
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 P35089
- Every structure of UniProt P35094
- Elsewhere: RCSB PDB 1IJD · PDBe 1IJD · UniProt P35089 · UniProt P35094
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.