Research workbench
Rba sphaeroides pufx-ko rc-LH1
Analyse Rba sphaeroides pufx-ko rc-LH1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VOY
- Type
- protein
- Length
- 2,479 residues
- Chains
- 37
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light-harvesting protein B-875 alpha chain; Light-harvesting protein B-875 beta chain…
- UniProt
- Q3J1A4, Q3J1A3, Q3J1A5, Q3J1A6, Q3J170
- Ligands
- BCL, BPH, U10, SPN, FE2
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 11 distinct chains · 55% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F, I, K, O, Q, S, U, W, Y, 9, 4, 6, C | Light-harvesting protein B-875 alpha chain | protein | 54 | 70% helix, 0% strand | Q3J1A4 |
| B, t, 5, 3 | Light-harvesting protein B-875 beta chain | protein | 45 | 71% helix, 0% strand | Q3J1A3 |
| E, G, J, N, P, R, T, V, X | Light-harvesting protein B-875 beta chain | protein | 43 | 74% helix, 0% strand | Q3J1A3 |
| Z | Light-harvesting protein B-875 beta chain | protein | 42 | 76% helix, 0% strand | Q3J1A3 |
| 1 | Light-harvesting protein B-875 alpha chain | protein | 53 | 70% helix, 0% strand | Q3J1A4 |
| 2 | Light-harvesting protein B-875 beta chain | protein | 40 | 80% helix, 0% strand | Q3J1A3 |
| 7 | Light-harvesting protein B-875 alpha chain | protein | 46 | 70% helix, 0% strand | Q3J1A4 |
| 8, 0 | Light-harvesting protein B-875 beta chain | protein | 44 | 73% helix, 0% strand | Q3J1A3 |
| L | Reaction center protein L chain | protein | 281 | 57% helix, 2% strand | Q3J1A5 |
| M | Reaction center protein M chain | protein | 305 | 60% helix, 2% strand | Q3J1A6 |
| H | Reaction center protein H chain | protein | 247 | 21% helix, 21% strand | Q3J170 |
Ligands and binding sites
- BCL · Bacteriochlorophyll A · ligand · 38 copies · chains 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, C, 7, 8, 4, t, 0, 6, 5, 3, L, M
- BPH · Bacteriopheophytin A · ligand · 2 copies · chains L, M
- U10 · Ubiquinone-10 · ligand · 2 copies · chains L, M
- SPN · Speroidenone · ligand · chains Y, 1, M
- FE2 · Fe (II) ion · metal · chains L, M
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 | 930 | 0.84 | 0.85 | 106 | SPN |
| 2 | 913 | 0.79 | 0.81 | 56 | BCL |
| 3 | 442 | 0.79 | 0.87 | 75 | U10, BPH |
| 4 | 515 | 0.76 | 0.83 | 49 | empty |
| 5 | 632 | 0.75 | 0.81 | 58 | empty |
Interfaces
105 interfaces between chains.
- L–M · 4726 Ų buried · 54 hydrogen bonds · protein-protein
- M–H · 2849 Ų buried · 32 hydrogen bonds · protein-protein
- L–H · 1500 Ų buried · 13 hydrogen bonds · protein-protein
- Q–R · 830 Ų buried · 8 hydrogen bonds · protein-protein
- 6–5 · 830 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- Q3J1A6 · AlphaFold monomer V2.0 prediction for reaction center protein M chain (Q3J1A6) · a predicted model of the same protein · chain M against A, TM-score 0.97
- Q3J1A5 · AlphaFold monomer V2.0 prediction for reaction center protein L chain (Q3J1A5) · a predicted model of the same protein · chain L against A, TM-score 0.95
- Q3J170 · AlphaFold monomer V2.0 prediction for reaction center protein H chain (Q3J170) · a predicted model of the same protein · chain H against A, TM-score 0.92
- Q3J1A3 · AlphaFold monomer V2.0 prediction for light-harvesting protein B-875 beta chain (Q3J1A3) · a predicted model of the same protein · chain 2 against A, TM-score 0.87
- Q3J1A4 · AlphaFold monomer V2.0 prediction for light-harvesting protein B-875 alpha chain (Q3J1A4) · a predicted model of the same protein · chain A against A, TM-score 0.62
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 Q3J1A4
- Every structure of UniProt Q3J1A3
- Every structure of UniProt Q3J1A5
- Every structure of UniProt Q3J1A6
- Every structure of UniProt Q3J170
- Elsewhere: RCSB PDB 7VOY · PDBe 7VOY · UniProt Q3J1A4 · UniProt Q3J1A3 · UniProt Q3J1A5 · UniProt Q3J1A6 · UniProt Q3J170
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