MolNFT v1 · #18738 · protein
Crystal structure of rc-LH1 core complex from rhodopseudomonas palustris
1PYH · Reaction center protein L chain: “Crystal structure of rc-LH1 core complex from rhodopseudomonas palustris”. X-ray diffraction, 3 ligands (BCL, BPH, FE), 12 pockets (best druggability 0.84). MolNFT v1 #18738 on GenesisL1: 3D…
- PDB
- 1PYH
- Type
- protein
- Length
- 1,690 residues
- Chains
- 34
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 · 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, G, F, I, H, J, K, L, M, N, O, P, Q, R, S, U, T, V, W, X, Y, 1, 2, 3, 4, 6, 5, 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 B against B, 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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