MolNFT v1 · #29469 · protein
Photosynthetic reaction center from rhodobacter sphaeroides
1Z9K · Reaction center protein L chain: “Photosynthetic reaction center from rhodobacter sphaeroides”. X-ray diffraction, 5 ligands (BCL, BPH, U10), 10 pockets (best druggability 0.81). MolNFT v1 #29469 on GenesisL1: 3D structure, binding…
- PDB
- 1Z9K
- Type
- protein
- Length
- 821 residues
- Chains
- 3
- 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, BPH, U10, FE, MN
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reaction center protein L chain | protein | 281 | 49% helix, 4% strand | P02954 |
| B | Reaction center protein M chain | protein | 302 | 51% helix, 2% strand | P02953 |
| C | Reaction center protein H chain | protein | 238 | 21% helix, 18% strand | P11846 |
Ligands and binding sites
- BCL · Bacteriochlorophyll A · ligand · 4 copies · chains A, B
- BPH · Bacteriopheophytin A · ligand · 2 copies · chains A, B
- U10 · Ubiquinone-10 · ligand · 2 copies · chains A, B
- FE · Fe (III) ion · metal · chains A, B
- MN · Manganese (II) ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1183 | 0.81 | 0.81 | 109 | BCL |
| 2 | 285 | 0.70 | 0.84 | 38 | U10 |
| 3 | 147 | 0.59 | 0.83 | 19 | empty |
| 4 | 156 | 0.55 | 0.81 | 31 | empty |
| 5 | 148 | 0.45 | 0.76 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 4603 Ų buried · 52 hydrogen bonds · protein-protein
- B–C · 2948 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1696 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1Z9K · Photosynthetic Reaction Center from Rhodobacter sphaeroides · the same entry in another collection · chain A against A, 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 1Z9K · PDBe 1Z9K · UniProt P02954 · UniProt P02953 · UniProt P11846
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