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Crystal structure of RC-LH1 core complex from Rhodopseudomonas palustris
Analyse Crystal structure of RC-LH1 core complex from Rhodopseudomonas palustris in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PYH
- Type
- protein
- Length
- 1,690 residues
- Chains
- 34
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.8
- Source
- Rhodopseudomonas palustris
- Molecule
- Reaction center protein L chain; Reaction center protein M chain; Reaction center protein…
- Ligands
- BCL, BPH, FE
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · resolution 4.8 · 5 distinct chains · 56% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reaction center protein L chain | protein | 281 | 64% helix, 4% strand | — |
| B | Reaction center protein M chain | protein | 302 | 66% helix, 4% strand | — |
| C | Reaction center protein H chain | protein | 241 | 26% helix, 24% strand | — |
| D, F, H, J, L, N, P, R, T, V, X, Z, 1, 3, 5, 7 | Light-harvesting protein B-800/850, alpha chain | protein | 26 | 85% helix, 0% strand | — |
| E, G, I, K, M, O, Q, S, U, W, Y, 2, 4, 6, 8 | Light-harvesting protein B-800/850, beta chain | protein | 30 | 93% helix, 0% strand | — |
Ligands and binding sites
- BCL · Bacteriochlorophyll A · ligand · 34 copies · chains A, B, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, 1, 2, 3, 4, 5, 6, 7, 8
- BPH · Bacteriopheophytin A · ligand · 2 copies · chains A, B
- FE · Fe (III) ion · metal
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 902 | 0.84 | 0.86 | 157 | empty |
| 2 | 329 | 0.77 | 0.88 | 59 | empty |
| 3 | 228 | 0.69 | 0.86 | 37 | FE |
| 4 | 86 | 0.56 | 0.86 | 30 | empty |
| 5 | 325 | 0.56 | 0.75 | 47 | empty |
Interfaces
23 interfaces between chains.
- A–B · 1677 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 947 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 711 Ų buried · 9 hydrogen bonds · protein-protein
- A–7 · 201 Ų buried · 0 hydrogen bonds · protein-protein
- C–F · 116 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1PYH · Crystal structure of rc-LH1 core complex from rhodopseudomonas palustris · the same entry in another collection · chain 2 against 2, 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
- Elsewhere: RCSB PDB 1PYH · PDBe 1PYH
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