MolNFT v1 · #21113 · protein
Photosynthetic reaction center double mutant from rhodobacter sphaeroides with asp L213 replaced with asn and arg M233 replaced with cys in the charge-neutral dqaqb state (tetragonal form)
1RZZ · Reaction center protein L chain: “Photosynthetic reaction center double mutant from rhodobacter sphaeroides with asp L213 replaced with asn and…”. X-ray diffraction, 5 ligands (BCL, U10, BPH), 20 pockets (best druggability 0.83).…
- PDB
- 1RZZ
- Type
- protein
- Length
- 1,652 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reaction center protein L chain; Reaction center protein M chain; Reaction center protein…
- UniProt
- P02954, P02953, P11846
- Ligands
- BCL, U10, BPH, SPO, FE2
- 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 | Reaction center protein L chain | protein | 281 | 62% helix, 4% strand | P02954 |
| M, S | Reaction center protein M chain | protein | 299 | 65% helix, 4% strand | P02953 |
| H, T | Reaction center protein H chain | protein | 246 | 27% helix, 24% strand | P11846 |
Ligands and binding sites
- BCL · Bacteriochlorophyll A · ligand · 8 copies · chains L, M, R, S
- U10 · Ubiquinone-10 · ligand · 4 copies · chains L, M, R, S
- BPH · Bacteriopheophytin A · ligand · 4 copies · chains L, M, R, S
- SPO · Spheroidene · ligand · 2 copies · chains M, S
- FE2 · Fe (II) ion · metal · 2 copies · chains L, M, R, S
- LDA · Lauryl dimethylamine-N-oxide · additive · 5 copies · chains M, H, L, S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 973 | 0.83 | 0.84 | 98 | BCL, BPH, SPO |
| 2 | 880 | 0.83 | 0.84 | 86 | BCL, BPH |
| 3 | 191 | 0.76 | 0.91 | 35 | U10 |
| 4 | 360 | 0.76 | 0.86 | 69 | empty |
| 5 | 233 | 0.69 | 0.85 | 28 | U10 |
Interfaces
6 interfaces between chains.
- L–M · 4555 Ų buried · 65 hydrogen bonds · protein-protein
- R–S · 4527 Ų buried · 65 hydrogen bonds · protein-protein
- M–H · 2769 Ų buried · 37 hydrogen bonds · protein-protein
- S–T · 2751 Ų buried · 38 hydrogen bonds · protein-protein
- L–H · 1641 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1RZZ · Photosynthetic reaction center double mutant from rhodobacter sphaeroides with asp L213… · the same entry in another collection · chain M against M, 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 1RZZ · PDBe 1RZZ · UniProt P02954 · UniProt P02953 · UniProt P11846
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