MolNFT v2 · #177051 · protein
Structure of photosynthetic LH1-rc super-complex of thiorhodovibrio strain 970
7C9R: “Structure of photosynthetic LH1-rc super-complex of thiorhodovibrio strain 970”. Electron microscopy at 2.82, 13 ligands (BCL, PGV, H4X). MolNFT v2 #177051 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7C9R
- Type
- protein
- Length
- 3,009 residues
- Chains
- 36
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.82
- Source
- Thiorhodovibrio sp. 970
- UniProt
- H8Z3S2, G1BIY6, G1BIY7, H8Z0X5, G1BIY5, G1BIY9, G1BIY4, H8Z3S4, H8Z3R9, G1BIZ0
- Ligands
- BCL, PGV, H4X, HEM, CDL, BPH, UQ8, 8K6, DGA, MQ8, CA, MG, FE
Structure
electron microscopy · resolution 2.82 · 21 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | — | protein | 311 | — | H8Z3S2 |
| L | — | protein | 272 | — | G1BIY6 |
| M | — | protein | 318 | — | G1BIY7 |
| H | — | protein | 257 | — | H8Z0X5 |
| A | — | protein | 70 | — | G1BIY5 |
| B | — | protein | 43 | — | G1BIY9 |
| D, F, K | — | protein | 72 | — | G1BIY5 |
| E, N, Z, 8 | — | protein | 42 | — | G1BIY4 |
| G, J, X, 2, 0 | — | protein | 41 | — | G1BIY4 |
| I, O | — | protein | 73 | — | G1BIY5 |
| P | — | protein | 42 | — | G1BIY9 |
| Q | — | protein | 78 | — | H8Z3S4 |
| R | — | protein | 44 | — | G1BIY4 |
| S | — | protein | 72 | — | H8Z3R9 |
| T, V, 6 | — | protein | 43 | — | G1BIY4 |
| U, 1 | — | protein | 72 | — | H8Z3R9 |
| W, Y | — | protein | 73 | — | H8Z3R9 |
| 3, 7 | — | protein | 73 | — | H8Z3R9 |
| 4 | — | protein | 44 | — | G1BIY9 |
| 5 | — | protein | 74 | — | H8Z3R9 |
| 9 | — | protein | 84 | — | G1BIZ0 |
Ligands and binding sites
- BCL · 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
- PGV · (1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11E)-octadec-11-enoate · ligand · 19 copies · chains C, M, L, H, K, O, Q, A, D, F, I, R, S, Y, 1, 3, 5, 9
- H4X · (6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E}, 22~{E},24~{E},26~{E})-2,31-dimethoxy-2,6,10,14,19,23, 27,31-octamethyl-dotriaconta-6,8,10,12,14,16,18,20,22, 24,26-undecaene · ligand · 17 copies · chains H, A, B, D, 9, E, F, G, I, J, K, N, O, M, Q, R, S, P, T, U, W, X, Y, V, Z, 1, 2, 3, 4, 5, 7, 8, 6, 0
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains C, M
- CDL · Cardiolipin · ligand · 3 copies · chains L, M, H, S, U, W, Y
- BPH · Bacteriopheophytin A · ligand · 2 copies · chains L, M
- UQ8 · Ubiquinone-8 · ligand · 2 copies · chains L, 5, 7
- 8K6 · Octadecane · ligand · 2 copies · chains L, 7, 9
- DGA · Diacyl glycerol · ligand · chains C, L
- MQ8 · Menaquinone 8 · ligand · chains L, M
- CA · Calcium ion · metal · 17 copies · chains C, A, 0, B, 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, 9
- MG · Magnesium ion · metal · chains C, M
- FE · Fe (III) ion · metal · chains L, M
- LMT · Dodecyl-beta-D-maltoside · additive · 18 copies · chains A, B, D, E, 0, F, G, I, J, K, N, O, P, R, S, T, U, V, W, X, Y, Z, 1, 2, 3, 4, 5, 6, 7, 8
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 7C9R · Structure of photosynthetic LH1-rc super-complex of thiorhodovibrio strain 970 · the same entry in another collection · chain 1 against 1, 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 H8Z3S2
- Every structure of UniProt G1BIY6
- Every structure of UniProt G1BIY7
- Every structure of UniProt H8Z0X5
- Every structure of UniProt G1BIY5
- Every structure of UniProt G1BIY9
- Every structure of UniProt G1BIY4
- Every structure of UniProt H8Z3S4
- Every structure of UniProt H8Z3R9
- Every structure of UniProt G1BIZ0
- Elsewhere: RCSB PDB 7C9R · PDBe 7C9R · UniProt H8Z3S2 · UniProt G1BIY6 · UniProt G1BIY7 · UniProt H8Z0X5 · UniProt G1BIY5 · UniProt G1BIY9 · UniProt G1BIY4 · UniProt H8Z3S4 · UniProt H8Z3R9 · UniProt G1BIZ0
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