MolNFT v1 · #174744 · protein
Co-crystal structure of a photosynthetic LH1-rc in complex with electron donor hipip
7C52 · Photosynthetic reaction center cytochrome C subunit: “Co-crystal structure of a photosynthetic LH1-rc in complex with electron donor hipip”. X-ray diffraction, 14 ligands (BCL, CRT, PGV), 20 pockets (best druggability 0.86). MolNFT…
- PDB
- 7C52
- Type
- protein
- Length
- 2,809 residues
- Chains
- 37
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosynthetic reaction center cytochrome C subunit; Photosynthetic reaction center L…
- UniProt
- D2Z0P5, D2Z0P3, A8ASG6, D2Z0P9, D2Z0P2, D2Z0P1, P80176
- Ligands
- BCL, CRT, PGV, CDL, PEF, UQ8, HEM, BPH, LHG, MQ8, SF4, CA, FE, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 17 distinct chains · 52% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Photosynthetic reaction center cytochrome C subunit | protein | 311 | 43% helix, 5% strand | D2Z0P5 |
| L | Photosynthetic reaction center L subunit | protein | 280 | 64% helix, 4% strand | D2Z0P3 |
| M | Photosynthetic reaction center M subunit | protein | 318 | 61% helix, 4% strand | A8ASG6 |
| H | Photosynthetic reaction center H subunit | protein | 255 | 25% helix, 22% strand | D2Z0P9 |
| A, 5 | LH1 alpha polypeptide | protein | 54 | 56% helix, 0% strand | D2Z0P2 |
| B, G, J, N, P, V, 4, 6 | LH1 beta polypeptide | protein | 42 | 76% helix, 0% strand | D2Z0P1 |
| D, F | LH1 alpha polypeptide | protein | 55 | 58% helix, 0% strand | D2Z0P2 |
| E | LH1 beta polypeptide | protein | 38 | 84% helix, 0% strand | D2Z0P1 |
| I, K, Q, Y, 7, 9 | LH1 alpha polypeptide | protein | 57 | 53% helix, 0% strand | D2Z0P2 |
| O, 1, 3 | LH1 alpha polypeptide | protein | 56 | 54% helix, 0% strand | D2Z0P2 |
| R, X, 2, 8 | LH1 beta polypeptide | protein | 41 | 78% helix, 0% strand | D2Z0P1 |
| S | LH1 alpha polypeptide | protein | 56 | 54% helix, 0% strand | D2Z0P2 |
| T, 0 | LH1 beta polypeptide | protein | 43 | 74% helix, 0% strand | D2Z0P1 |
| U | LH1 alpha polypeptide | protein | 58 | 60% helix, 0% strand | D2Z0P2 |
| W | LH1 alpha polypeptide | protein | 56 | 57% helix, 0% strand | D2Z0P2 |
| Z | LH1 beta polypeptide | protein | 40 | 80% helix, 0% strand | D2Z0P1 |
| b | High-potential iron-sulfur protein | protein | 83 | 19% helix, 23% strand | P80176 |
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, B, 9, G, I, J, K, N, Q, R, S, P, T, U, V, W, X, Y, Z, 1, 2, 3, 5, 6, 7, 4, 8, 0
- 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, F, Y, 1, 3, 5, 9
- CDL · Cardiolipin · ligand · 10 copies · chains L, M, H, F, K, A, D, O, Q, S, U, W, Y, 1
- PEF · Di-palmitoyl-3-sn-phosphatidylethanolamine · ligand · 10 copies · chains M, H, I, K, U, W, 1, 3, 5
- UQ8 · Ubiquinone-8 · ligand · 5 copies · chains L, H, 5, 6, 7, 9, M, S
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains C, b, 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
- SF4 · Iron/sulfur cluster · ligand · chains b
- CA · Calcium ion · metal · 17 copies · chains C, M, 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
- FE · Fe (III) ion · metal · chains L, M
- SO4 · Sulfate ion · ion · chains L, M, W
- GOL · Glycerol · additive · 2 copies · chains C, L, H
- LMT · Dodecyl-beta-D-maltoside · additive · 2 copies · chains C, M, H, D, F, I
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 | 733 | 0.86 | 0.89 | 105 | HEM |
| 2 | 934 | 0.84 | 0.85 | 89 | UQ8, CRT |
| 3 | 893 | 0.83 | 0.85 | 99 | BCL |
| 4 | 703 | 0.81 | 0.85 | 70 | PEF, CRT, CDL |
| 5 | 907 | 0.80 | 0.81 | 87 | GOL, CRT, PGV |
Interfaces
117 interfaces between chains.
- L–M · 4577 Ų buried · 63 hydrogen bonds · protein-protein
- M–H · 2810 Ų buried · 45 hydrogen bonds · protein-protein
- C–M · 2452 Ų buried · 41 hydrogen bonds · protein-protein
- L–H · 1723 Ų buried · 19 hydrogen bonds · protein-protein
- C–L · 1635 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 3 covalent (heme attachment, covalent ligand).
Compared structures
- 7C52 · Co-crystal structure of a photosynthetic LH1-RC in complex with electron donor HiPIP · the same entry in another collection · chain I against I, 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
- Every structure of UniProt P80176
- Elsewhere: RCSB PDB 7C52 · PDBe 7C52 · UniProt D2Z0P5 · UniProt D2Z0P3 · UniProt A8ASG6 · UniProt D2Z0P9 · UniProt D2Z0P2 · UniProt D2Z0P1 · UniProt P80176
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