Research workbench
Structure of photosynthetic LH1-rc super-complex of allochromatium tepidum
Analyse Structure of photosynthetic LH1-rc super-complex of allochromatium tepidum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VRJ
- Type
- protein
- Length
- 2,604 residues
- Chains
- 36
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosynthetic reaction center cytochrome C subunit; Photosynthetic reaction center L…
- Ligands
- BCL, CRT, PGV, CDL, HEC, UQ8, BPH, MQ8, DGA, PLM, CA, MG, FE
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 22 distinct chains · 55% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Photosynthetic reaction center cytochrome C subunit | protein | 313 | 39% helix, 6% strand | — |
| L | Photosynthetic reaction center L subunit | protein | 277 | 62% helix, 4% strand | — |
| M | Photosynthetic reaction center M subunit | protein | 318 | 58% helix, 4% strand | — |
| H | Photosynthetic reaction center H subunit | protein | 259 | 24% helix, 23% strand | — |
| A, I, K, O, Q, 1, 7 | Light-harvesting protein LH1 ALPHA2 | protein | 44 | 64% helix, 0% strand | — |
| B | Light-harvesting protein LH1 BETA1 | protein | 44 | 73% helix, 0% strand | — |
| D | Light-harvesting protein LH1 ALPHA1 | protein | 50 | 64% helix, 0% strand | — |
| E | Light-harvesting protein LH1 BETA3 | protein | 43 | 70% helix, 0% strand | — |
| F | Light-harvesting protein LH1 ALPHA1 | protein | 49 | 63% helix, 0% strand | — |
| G, T, V, X | Light-harvesting protein LH1 BETA3 | protein | 42 | 76% helix, 0% strand | — |
| J | Light-harvesting protein LH1 BETA1 | protein | 40 | 75% helix, 0% strand | — |
| N, 6 | Light-harvesting protein LH1 BETA1 | protein | 38 | 84% helix, 0% strand | — |
| P, 4, 0 | Light-harvesting protein LH1 BETA1 | protein | 42 | 76% helix, 0% strand | — |
| R, 2 | Light-harvesting protein LH1 BETA1 | protein | 41 | 76% helix, 0% strand | — |
| S | Light-harvesting protein LH1 ALPHA1 | protein | 52 | 58% helix, 0% strand | — |
| U | Light-harvesting protein LH1 ALPHA1 | protein | 51 | 63% helix, 0% strand | — |
| W | Light-harvesting protein LH1 ALPHA1 | protein | 56 | 54% helix, 0% strand | — |
| Y | Light-harvesting protein LH1 ALPHA1 | protein | 63 | 52% helix, 0% strand | — |
| Z | Light-harvesting protein LH1 BETA3 | protein | 41 | 78% helix, 0% strand | — |
| 3 | Light-harvesting protein LH1 ALPHA3 | protein | 65 | 52% helix, 0% strand | — |
| 5, 9 | Light-harvesting protein LH1 ALPHA2 | protein | 43 | 65% helix, 0% strand | — |
| 8 | Light-harvesting protein LH1 BETA1 | protein | 37 | 78% helix, 0% strand | — |
Ligands and binding sites
- BCL · Bacteriochlorophyll A · ligand · 36 copies · chains L, M, A, B, 9, D, E, F, G, I, J, K, N, P, O, 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, S, T, U, R, V, W, X, Y, Z, 1, 2, 3, 4, 5, 6, 7, 0, 8
- PGV · (1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11E)-octadec-11-enoate · ligand · 12 copies · chains C, L, 1, 3, Y, A, D, H, 9, M, S, K, O, Q, F, I, 5
- CDL · Cardiolipin · ligand · 8 copies · chains L, M, H, A, D, F, I, Q, R, S
- HEC · Heme C · ligand · 4 copies · chains C, L, M
- UQ8 · Ubiquinone-8 · ligand · 3 copies · chains L, 5, 6, 7, 9
- BPH · Bacteriopheophytin A · ligand · 2 copies · chains L, M
- MQ8 · Menaquinone 8 · ligand · 2 copies · chains L, M, U, W
- DGA · Diacyl glycerol · ligand · chains C, L, 3
- PLM · Palmitic acid · ligand · chains C, L
- CA · Calcium ion · metal · 6 copies · chains B, D, E, F, R, S, T, U, V, W, X, Y
- MG · Magnesium ion · metal · chains C, M
- FE · Fe (III) ion · metal · chains L, M
- LMT · Dodecyl-beta-D-maltoside · additive · 18 copies · chains C, M, H, I, B, 0, E, G, J, N, K, O, P, R, T, V, X, Y, Z, 2, 3, 4, 6, 8
- LDA · Lauryl dimethylamine-N-oxide · additive · 2 copies · chains M, K, O
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 | 1195 | 0.89 | 0.89 | 108 | HEC |
| 2 | 670 | 0.87 | 0.91 | 96 | UQ8 |
| 3 | 1191 | 0.82 | 0.82 | 97 | BCL |
| 4 | 931 | 0.81 | 0.82 | 80 | UQ8 |
| 5 | 544 | 0.76 | 0.82 | 50 | CRT, LDA |
Interfaces
117 interfaces between chains.
- L–M · 4571 Ų buried · 49 hydrogen bonds · protein-protein
- M–H · 2820 Ų buried · 36 hydrogen bonds · protein-protein
- C–M · 2396 Ų buried · 27 hydrogen bonds · protein-protein
- L–H · 1732 Ų buried · 19 hydrogen bonds · protein-protein
- C–L · 1564 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified, 6 cofactor, 1 covalent, 1 lipid (formylation, heme c attachment, covalent ligand, palmitoylation).
Compared structures
- 7VRJ · STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF Allochromatium tepidum · the same entry in another collection · chain L against L, 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 7VRJ · PDBe 7VRJ
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