MolNFT v1 · #184668 · protein
Cryo-EM structure of the rhodospirillum rubrum rc-LH1 complex
7OY8 · Light-harvesting protein B-870 beta chain: “Cryo-EM structure of the rhodospirillum rubrum rc-LH1 complex”. Electron microscopy, 10 ligands (07D, CRT, U10), 20 pockets (best druggability 0.81). MolNFT v1 #184668 on GenesisL1: 3D…
- PDB
- 7OY8
- Type
- protein
- Length
- 2,293 residues
- Chains
- 35
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light-harvesting protein B-870 beta chain; Antenna complex, ALPHA/BETA subunit…
- UniProt
- Q2RQ23, Q2RQ24, Q2RWS4, Q2RQ25, Q2RQ26
- Ligands
- 07D, CRT, U10, PGW, CD4, BPH, RQ0, FE, CL, PO4
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 12 distinct chains · 57% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1, 3, 5, 7, I, O, U, W, d, n | Light-harvesting protein B-870 beta chain | protein | 44 | 73% helix, 5% strand | Q2RQ23 |
| 2, A, E, J, N, V | Antenna complex, ALPHA/BETA subunit | protein | 46 | 63% helix, 0% strand | Q2RQ24 |
| 4, 6, D, F, G, T, X, Z | Antenna complex, ALPHA/BETA subunit | protein | 47 | 62% helix, 0% strand | Q2RQ24 |
| 8 | Antenna complex, ALPHA/BETA subunit | protein | 48 | 56% helix, 0% strand | Q2RQ24 |
| 9 | Light-harvesting protein B-870 beta chain | protein | 46 | 70% helix, 4% strand | Q2RQ23 |
| H | Photosynthetic reaction center, H-chain | protein | 257 | 26% helix, 24% strand | Q2RWS4 |
| K, S, m | Light-harvesting protein B-870 beta chain | protein | 45 | 71% helix, 4% strand | Q2RQ23 |
| L | Photosynthetic reaction center L subunit | protein | 274 | 66% helix, 4% strand | Q2RQ25 |
| M | Reaction center protein M chain | protein | 305 | 64% helix, 5% strand | Q2RQ26 |
| Q | Light-harvesting protein B-870 beta chain | protein | 47 | 68% helix, 4% strand | Q2RQ23 |
| R | Antenna complex, ALPHA/BETA subunit | protein | 46 | 63% helix, 0% strand | Q2RQ24 |
| Y | Light-harvesting protein B-870 beta chain | protein | 43 | 74% helix, 5% strand | Q2RQ23 |
Ligands and binding sites
- 07D · Trans-Geranyl BACTERIOCHLOROPHYLL A · ligand · 37 copies · chains 1, X, Z, n, 2, 3, 4, 5, 6, M, 7, 8, 9, D, A, R, W, E, I, F, K, G, H, O, Q, J, N, S, U, L, T, Y, V, d, m
- CRT · Spirilloxanthin · ligand · 17 copies · chains 1, 2, X, Z, 3, 4, 5, 6, 7, 8, 9, D, E, I, A, J, N, U, F, K, M, R, W, G, O, Q, S, T, Y, V, d, m, n
- U10 · Ubiquinone-10 · ligand · 3 copies · chains L, M, A, N, R, J
- PGW · (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate · ligand · 2 copies · chains H, L, M, G, J
- 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 · 2 copies · chains H, J, L, M, D, E
- BPH · Bacteriopheophytin A · ligand · 2 copies · chains L, M, 4
- RQ0 · 2-azanyl-5-[(2~{E},6~{E},8~{E},10~{E},12~{E},14~{E}, 18~{E},22~{E},26~{E},30~{E},34~{E})-3,7,11,15,19,23, 27,31,35,39-decamethyltetraconta-2,6,8,10,12,14,18,22, 26,30,34,38-dodecaenyl]-3-methoxy-6-methyl-cyclohexa-2,5-diene-1,4-dione · ligand · chains L, M
- FE · Fe (III) ion · metal · chains L, M
- CL · Chloride ion · ion · chains H, M
- PO4 · Phosphate ion · ion · chains 8, M
- LMT · Dodecyl-beta-D-maltoside · additive · chains L, R, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1200 | 0.81 | 0.82 | 96 | BPH, 07D |
| 2 | 195 | 0.80 | 0.95 | 44 | empty |
| 3 | 827 | 0.80 | 0.82 | 81 | CRT, PO4 |
| 4 | 981 | 0.77 | 0.79 | 76 | U10 |
| 5 | 1190 | 0.75 | 0.78 | 105 | CRT |
Interfaces
98 interfaces between chains.
- L–M · 4472 Ų buried · 58 hydrogen bonds · protein-protein
- H–M · 2901 Ų buried · 44 hydrogen bonds · protein-protein
- H–L · 1578 Ų buried · 22 hydrogen bonds · protein-protein
- G–Q · 837 Ų buried · 10 hydrogen bonds · protein-protein
- 6–M · 797 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (formylation).
Compared structures
- 7OY8 · Cryo-EM structure of the Rhodospirillum rubrum RC-LH1 complex · 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 Q2RQ23
- Every structure of UniProt Q2RQ24
- Every structure of UniProt Q2RWS4
- Every structure of UniProt Q2RQ25
- Every structure of UniProt Q2RQ26
- Elsewhere: RCSB PDB 7OY8 · PDBe 7OY8 · UniProt Q2RQ23 · UniProt Q2RQ24 · UniProt Q2RWS4 · UniProt Q2RQ25 · UniProt Q2RQ26
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