Research workbench
Structure of photosynthetic LH1-rc super-complex of rhodospirillum rubrum
Analyse Structure of photosynthetic LH1-rc super-complex of rhodospirillum rubrum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EQD
- Type
- protein
- Length
- 2,302 residues
- Chains
- 35
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reaction center protein L chain; Reaction center protein M chain; Photoreaction center…
- UniProt
- P10717, Q2RQ26, Q7M149, P02947, Q2RQ23
- Ligands
- 07D, CRT, CDL, PEF, 08I, U10, PGV, RQ0, FE
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 6 distinct chains · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Reaction center protein L chain | protein | 275 | 62% helix, 5% strand | P10717 |
| M | Reaction center protein M chain | protein | 304 | 63% helix, 5% strand | Q2RQ26 |
| H | Photoreaction center protein H | protein | 256 | 22% helix, 23% strand | Q7M149 |
| A, D, F, I, K, O, Q, S, U, W, Y, 1, 3, 5, 7, 9 | Light-harvesting protein B-870 alpha chain | protein | 47 | 64% helix, 0% strand | P02947 |
| B, G, J, N, R, T, V, X, 4, 6, 0 | Light-harvesting protein B-870 beta chain | protein | 45 | 71% helix, 4% strand | Q2RQ23 |
| E, P, Z, 2, 8 | Light-harvesting protein B-870 beta chain | protein | 44 | 66% helix, 5% strand | Q2RQ23 |
Ligands and binding sites
- 07D · Trans-Geranyl BACTERIOCHLOROPHYLL A · ligand · 36 copies · chains L, M, A, B, 9, D, E, F, G, I, J, K, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, 1, 2, 3, 4, 5, 6, 7, 8, 0
- CRT · Spirilloxanthin · ligand · 17 copies · chains M, O, Q, A, B, D, 9, E, F, G, I, J, K, N, P, R, S, T, U, V, W, X, Y, Z, 1, 2, 3, 4, 5, 6, 7, 8, 0
- CDL · Cardiolipin · ligand · 5 copies · chains L, M, H, K, O, D, F, I
- PEF · Di-palmitoyl-3-sn-phosphatidylethanolamine · ligand · 3 copies · chains H, D, M, I, K, O
- 08I · Trans-Geranyl BACTERIOPHEOPHYTIN A · ligand · 2 copies · chains L, M
- U10 · Ubiquinone-10 · ligand · 2 copies · chains L, M
- PGV · (1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11E)-octadec-11-enoate · ligand · 2 copies · chains L, A, D, M, H
- 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, A
- FE · Fe (III) ion · metal · chains L, M
- LMT · Dodecyl-beta-D-maltoside · additive · 23 copies · chains L, M, O, Q, H, I, K, B, E, G, J, N, P, R, T, V, X, Z, 2, 4, 6, 3, 5, 8, 7, 0
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 | 1145 | 0.82 | 0.83 | 91 | 07D, 08I |
| 2 | 937 | 0.80 | 0.81 | 100 | CRT, LMT |
| 3 | 310 | 0.78 | 0.89 | 54 | empty |
| 4 | 1047 | 0.77 | 0.79 | 86 | LMT, CRT |
| 5 | 820 | 0.77 | 0.80 | 82 | CRT |
Interfaces
98 interfaces between chains.
- L–M · 4425 Ų buried · 62 hydrogen bonds · protein-protein
- M–H · 2819 Ų buried · 41 hydrogen bonds · protein-protein
- L–H · 1619 Ų buried · 23 hydrogen bonds · protein-protein
- M–Q · 832 Ų buried · 2 hydrogen bonds · protein-protein
- F–G · 829 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (formylation).
Compared structures
- 7EQD · Structure of photosynthetic LH1-rc super-complex of rhodospirillum rubrum · the same entry in another collection · chain J against J, 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 P10717
- Every structure of UniProt Q2RQ26
- Every structure of UniProt Q7M149
- Every structure of UniProt P02947
- Every structure of UniProt Q2RQ23
- Elsewhere: RCSB PDB 7EQD · PDBe 7EQD · UniProt P10717 · UniProt Q2RQ26 · UniProt Q7M149 · UniProt P02947 · UniProt Q2RQ23
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