Research workbench
Photosynthetic reaction center from rhodobacter sphaeroides in the D+QB-charge separated state
Analyse Photosynthetic reaction center from rhodobacter sphaeroides in the D+QB-charge… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1AIG
- Type
- protein
- Length
- 1,656 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosynthetic reaction center (L subunit); Photosynthetic reaction center (M subunit)…
- UniProt
- P02954, P02953, P11846
- Ligands
- BCL, BPH, U10, FE2
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, N | Photosynthetic reaction center (L subunit) | protein | 281 | 61% helix, 3% strand | P02954 |
| M, O | Photosynthetic reaction center (M subunit) | protein | 299 | 65% helix, 4% strand | P02953 |
| H, P | Photosynthetic reaction center (H subunit) | protein | 248 | 25% helix, 24% strand | P11846 |
Ligands and binding sites
- BCL · Bacteriochlorophyll A · ligand · 8 copies · chains L, M, N, O
- BPH · Bacteriopheophytin A · ligand · 4 copies · chains L, M, N, O
- U10 · Ubiquinone-10 · ligand · 4 copies · chains L, M, H, N, O
- FE2 · Fe (II) ion · metal · 2 copies · chains L, M, N, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 968 | 0.84 | 0.84 | 92 | BCL |
| 2 | 941 | 0.83 | 0.84 | 83 | BCL |
| 3 | 107 | 0.76 | 0.96 | 33 | empty |
| 4 | 74 | 0.74 | 0.99 | 27 | empty |
| 5 | 128 | 0.70 | 0.90 | 21 | empty |
Interfaces
6 interfaces between chains.
- L–M · 4600 Ų buried · 71 hydrogen bonds · protein-protein
- N–O · 4574 Ų buried · 69 hydrogen bonds · protein-protein
- M–H · 2808 Ų buried · 45 hydrogen bonds · protein-protein
- O–P · 2791 Ų buried · 40 hydrogen bonds · protein-protein
- L–H · 1610 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 1AIG · Photosynthetic reaction center from rhodobacter sphaeroides in the D+QB-charge separated… · the same entry in another collection · chain L against L, 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 P02954
- Every structure of UniProt P02953
- Every structure of UniProt P11846
- Elsewhere: RCSB PDB 1AIG · PDBe 1AIG · UniProt P02954 · UniProt P02953 · UniProt P11846
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