MolNFT v2 · #190631 · protein
Cryo-EM structure of the Rhodobacter sphaeroides RC-LH1-PufXY monomer complex at 2.5 A
7PIL: “Cryo-EM structure of the Rhodobacter sphaeroides RC-LH1-PufXY monomer complex at 2.5 A”. Electron microscopy at 2.5, 8 ligands (BCL, SPO, 3PE). MolNFT v2 #190631 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7PIL
- Type
- protein
- Length
- 2,291 residues
- Chains
- 33
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- UniProt
- Q3J1A4, Q3J1A3, Q3J170, Q3J1A5, Q3J1A6, U5NME9, P13402
- Ligands
- BCL, SPO, 3PE, BPH, U10, UQ1, CD4, FE
Structure
electron microscopy · resolution 2.5 · 11 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| AA | — | protein | 46 | — | Q3J1A4 |
| AB, AC, AD, AE, AF, AG, AH, AI, AJ, AK, AL, AM | — | protein | 55 | — | Q3J1A4 |
| AN | — | protein | 51 | — | Q3J1A4 |
| BA, BB, BD, BE, BF, BG, BH, BI, BJ, BK, BL, BM | — | protein | 43 | — | Q3J1A3 |
| BC | — | protein | 42 | — | Q3J1A3 |
| BN | — | protein | 38 | — | Q3J1A3 |
| H | — | protein | 246 | — | Q3J170 |
| L | — | protein | 281 | — | Q3J1A5 |
| M | — | protein | 307 | — | Q3J1A6 |
| UU | — | protein | 49 | — | U5NME9 |
| X | — | protein | 55 | — | P13402 |
Ligands and binding sites
- BCL · Bacteriochlorophyll A · ligand · 32 copies · chains AA, BA, X, AB, BB, AC, BC, AD, BD, AE, BE, AF, BF, AG, BG, AH, BH, AI, BI, AJ, BJ, AK, BK, AL, BL, AM, BM, AN, BN, L, M
- SPO · Spheroidene · ligand · 26 copies · chains AA, AB, AC, BA, BB, AD, BC, AE, BD, AF, BE, AG, BF, AH, BG, AI, BH, AJ, BI, AK, BJ, AL, BK, AM, BL, AN, BM, X, M
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 4 copies · chains AB, AC, AD, H, L, M
- BPH · Bacteriopheophytin A · ligand · 2 copies · chains L, M
- U10 · Ubiquinone-10 · ligand · 2 copies · chains L, M, UU, AB, AC
- UQ1 · Ubiquinone-1 · ligand · chains L, M
- CD4 · (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate · ligand · chains AG, H, L, M
- FE · Fe (III) ion · metal · chains L, M
- LMT · Dodecyl-beta-D-maltoside · additive · 4 copies · chains AA, L, AB, AJ, AK, M, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- Q3J1A3 · AlphaFold monomer V2.0 prediction for light-harvesting protein B-875 beta chain (Q3J1A3) · a predicted model of the same protein · chain BN against A, TM-score 0.88
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 Q3J1A4
- Every structure of UniProt Q3J1A3
- Every structure of UniProt Q3J170
- Every structure of UniProt Q3J1A5
- Every structure of UniProt Q3J1A6
- Every structure of UniProt U5NME9
- Every structure of UniProt P13402
- Elsewhere: RCSB PDB 7PIL · PDBe 7PIL · UniProt Q3J1A4 · UniProt Q3J1A3 · UniProt Q3J170 · UniProt Q3J1A5 · UniProt Q3J1A6 · UniProt U5NME9 · UniProt P13402
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