Research workbench
Photosynthetic reaction center from rhodobacter sphaeroides in the charge-separated D+QAQB-state with the proton transfer inhibitor CD2+
Analyse Photosynthetic reaction center from rhodobacter sphaeroides in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DV3
- Type
- protein
- Length
- 1,652 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Photosynthetic reaction center reaction center
- UniProt
- P02954, P02953, P11846
- Ligands
- BCL, BPH, U10, FE2, CD, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, R | Photosynthetic reaction center reaction center | protein | 281 | 62% helix, 4% strand | P02954 |
| M, S | Photosynthetic reaction center reaction center | protein | 299 | 63% helix, 4% strand | P02953 |
| H, T | Photosynthetic reaction center reaction center | protein | 246 | 26% helix, 24% strand | P11846 |
Ligands and binding sites
- BCL · Bacteriochlorophyll A · ligand · 8 copies · chains L, M, R, S
- BPH · Bacteriopheophytin A · ligand · 4 copies · chains L, M, R, S
- U10 · Ubiquinone-10 · ligand · 4 copies · chains L, M, R, S
- FE2 · Fe (II) ion · metal · 2 copies · chains L, M, R, S
- CD · Cadmium ion · metal · 2 copies · chains H, T
- CL · Chloride ion · ion · 2 copies · chains L, M, R, S
- LDA · Lauryl dimethylamine-N-oxide · additive · 2 copies · chains M, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 931 | 0.83 | 0.84 | 91 | BCL, BPH |
| 2 | 787 | 0.81 | 0.84 | 69 | BCL |
| 3 | 138 | 0.77 | 0.95 | 34 | empty |
| 4 | 114 | 0.77 | 0.97 | 34 | empty |
| 5 | 239 | 0.76 | 0.89 | 44 | U10 |
Interfaces
6 interfaces between chains.
- R–S · 4540 Ų buried · 66 hydrogen bonds · protein-protein
- L–M · 4521 Ų buried · 66 hydrogen bonds · protein-protein
- M–H · 2751 Ų buried · 39 hydrogen bonds · protein-protein
- S–T · 2725 Ų buried · 40 hydrogen bonds · protein-protein
- L–H · 1590 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 1DV3 · Photosynthetic reaction center from rhodobacter sphaeroides in the 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 1DV3 · PDBe 1DV3 · UniProt P02954 · UniProt P02953 · UniProt P11846
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