Research workbench
PucD-LH2 complex from Rps. palustris
Analyse PucD-LH2 complex from Rps. palustris in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZE3
- Type
- protein
- Length
- 967 residues
- Chains
- 19
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Rhodopseudomonas palustris
- Molecule
- Light-harvesting protein B-800-850 alpha chain; Light-harvesting protein B-800-850 beta…
- UniProt
- A0A2R4GW23, A0A2R4GVX2, A0A2R4GRK2
- Ligands
- BCL, ZE0
- Pockets
- 16 · best druggability 0.74
Structure
electron microscopy · resolution 2.7 · 3 distinct chains · 37% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O, Q | Light-harvesting protein B-800-850 alpha chain | protein | 48 | 73% helix, 0% strand | A0A2R4GW23 |
| B, D, F, H, J, L, N, P, R | Light-harvesting protein B-800-850 beta chain | protein | 49 | 71% helix, 0% strand | A0A2R4GVX2 |
| S | PucA-LH2-gamma | protein | 94 | 0% helix, 0% strand | A0A2R4GRK2 |
Ligands and binding sites
- BCL · Bacteriochlorophyll A · ligand · 33 copies · chains A, B, Q, S, C, D, F, N, P, R, E, G, H, I, J, K, L, M, O
- ZE0 · (3'E)-3',4'-didehydro-1,2-dihydro-psi,psi-caroten-1-ol · ligand · 9 copies · chains A, B, C, D, E, Q, R, F, G, H, I, J, K, L, M, N, O, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 738 | 0.74 | 0.79 | 63 | ZE0 |
| 2 | 676 | 0.72 | 0.79 | 55 | ZE0 |
| 3 | 687 | 0.72 | 0.78 | 50 | ZE0 |
| 4 | 642 | 0.71 | 0.78 | 51 | ZE0 |
| 5 | 669 | 0.71 | 0.78 | 50 | ZE0 |
Interfaces
58 interfaces between chains.
- K–L · 687 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 687 Ų buried · 8 hydrogen bonds · protein-protein
- M–N · 685 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 682 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 680 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (carboxylation).
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 A0A2R4GW23
- Every structure of UniProt A0A2R4GVX2
- Every structure of UniProt A0A2R4GRK2
- Elsewhere: RCSB PDB 7ZE3 · PDBe 7ZE3 · UniProt A0A2R4GW23 · UniProt A0A2R4GVX2 · UniProt A0A2R4GRK2
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