MolNFT v1 · #140284 · protein
Structure of photosynthetic LH1-rc super-complex at 1.9 ångström resolution
5Y5S: “Structure of photosynthetic LH1-rc super-complex at 1.9 ångström resolution”. X-ray diffraction, 15 ligands (BCL, CRT, UNL). MolNFT v1 #140284 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5Y5S
- Type
- protein
- Length
- 2,726 residues
- Chains
- 36
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- D2Z0P5, D2Z0P3, A8ASG6, D2Z0P9, D2Z0P2, D2Z0P1
- Ligands
- BCL, CRT, UNL, PEF, PGV, CDL, UQ8, HEC, BPH, LHG, MQ8, CA, MG, FE, SO4
Structure
x-ray diffraction · 16 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | — | protein | 311 | — | D2Z0P5 |
| L | — | protein | 280 | — | D2Z0P3 |
| M | — | protein | 318 | — | A8ASG6 |
| H | — | protein | 255 | — | D2Z0P9 |
| A, 5 | — | protein | 54 | — | D2Z0P2 |
| B, G, J, N, P, V, 4, 6 | — | protein | 42 | — | D2Z0P1 |
| D, F | — | protein | 55 | — | D2Z0P2 |
| E | — | protein | 38 | — | D2Z0P1 |
| I, K, Q, Y, 7, 9 | — | protein | 57 | — | D2Z0P2 |
| O, 1, 3 | — | protein | 56 | — | D2Z0P2 |
| R, X, 2, 8 | — | protein | 41 | — | D2Z0P1 |
| S | — | protein | 56 | — | D2Z0P2 |
| T, 0 | — | protein | 43 | — | D2Z0P1 |
| U | — | protein | 58 | — | D2Z0P2 |
| W | — | protein | 56 | — | D2Z0P2 |
| Z | — | protein | 40 | — | D2Z0P1 |
Ligands and binding sites
- BCL · Bacteriochlorophyll A · ligand · 36 copies · chains L, M, A, B, 9, 0, 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
- CRT · Spirilloxanthin · ligand · 17 copies · chains M, O, A, D, E, F, G, I, J, K, N, Q, R, S, P, T, U, W, X, Y, V, Z, 1, 3, 4, 5, 2, 6, 7, B, 9, 8, 0
- UNL · Unknown ligand · ligand · 16 copies · chains L, M, B, 0, E, G, J, N, P, R, T, V, X, Z, 2, 4, 6, 8
- PEF · Di-palmitoyl-3-sn-phosphatidylethanolamine · ligand · 13 copies · chains M, O, H, F, I, K, U, W, 1, 3, 5
- PGV · (1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11E)-octadec-11-enoate · ligand · 10 copies · chains C, L, A, D, H, M, S, 9, F, Y, 1, 3, 5
- CDL · Cardiolipin · ligand · 9 copies · chains M, H, A, D, L, F, K, O, Q, S, U, W, Y, 1
- UQ8 · Ubiquinone-8 · ligand · 5 copies · chains L, 5, 6, 7, M, S, 9
- HEC · Heme C · ligand · 4 copies · chains C, L, M
- BPH · Bacteriopheophytin A · ligand · 2 copies · chains L, M
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · chains C, L
- MQ8 · Menaquinone 8 · ligand · chains L, M, A
- CA · Calcium ion · metal · 16 copies · chains 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
- FE · Fe (III) ion · metal · chains L, M
- SO4 · Sulfate ion · ion · 3 copies · chains L, M
- LDA · Lauryl dimethylamine-N-oxide · additive · 5 copies · chains M, K, H, I, J, N, O, T, V
- GOL · Glycerol · additive · 2 copies · chains C, L, H
- LMT · Dodecyl-beta-D-maltoside · additive · 2 copies · chains C, M, H, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 5Y5S · Structure of photosynthetic LH1-RC super-complex at 1.9 angstrom resolution · the same entry in another collection · chain C against C, 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 D2Z0P5
- Every structure of UniProt D2Z0P3
- Every structure of UniProt A8ASG6
- Every structure of UniProt D2Z0P9
- Every structure of UniProt D2Z0P2
- Every structure of UniProt D2Z0P1
- Elsewhere: RCSB PDB 5Y5S · PDBe 5Y5S · UniProt D2Z0P5 · UniProt D2Z0P3 · UniProt A8ASG6 · UniProt D2Z0P9 · UniProt D2Z0P2 · UniProt D2Z0P1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.