MolNFT v1 · #189701 · protein
Structure of photosynthetic LH1-rc super-complex of allochromatium tepidum
7VRJ: “Structure of photosynthetic LH1-rc super-complex of allochromatium tepidum”. Electron microscopy, 13 ligands (BCL, CRT, PGV). MolNFT v1 #189701 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7VRJ
- Type
- protein
- Length
- 2,604 residues
- Chains
- 36
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Ligands
- BCL, CRT, PGV, CDL, HEC, UQ8, BPH, MQ8, DGA, PLM, CA, MG, FE
Structure
electron microscopy · 22 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | — | protein | 313 | — | — |
| L | — | protein | 277 | — | — |
| M | — | protein | 318 | — | — |
| H | — | protein | 259 | — | — |
| A, I, K, O, Q, 1, 7 | — | protein | 44 | — | — |
| B | — | protein | 44 | — | — |
| D | — | protein | 50 | — | — |
| E | — | protein | 43 | — | — |
| F | — | protein | 49 | — | — |
| G, T, V, X | — | protein | 42 | — | — |
| J | — | protein | 40 | — | — |
| N, 6 | — | protein | 38 | — | — |
| P, 4, 0 | — | protein | 42 | — | — |
| R, 2 | — | protein | 41 | — | — |
| S | — | protein | 52 | — | — |
| U | — | protein | 51 | — | — |
| W | — | protein | 56 | — | — |
| Y | — | protein | 63 | — | — |
| Z | — | protein | 41 | — | — |
| 3 | — | protein | 65 | — | — |
| 5, 9 | — | protein | 43 | — | — |
| 8 | — | protein | 37 | — | — |
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, O, F, 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
- FE · Fe (III) ion · metal · chains L, M
- LMT · Dodecyl-beta-D-maltoside · additive · 18 copies · chains C, M, H, I, B, E, G, J, N, K, O, P, R, T, V, X, Z, 2, 3, 4, 6, 8, 0
- LDA · Lauryl dimethylamine-N-oxide · additive · 2 copies · chains K, M, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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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