MolNFT v1 · #32349 · protein
Lipidic cubic phase grown reaction centre from rhodobacter sphaeroides, ground state
2BNP · Reaction center protein L chain: “Lipidic cubic phase grown reaction centre from rhodobacter sphaeroides, ground state”. X-ray diffraction, 7 ligands (BCL, BPH, MST), 13 pockets (best druggability 0.81). MolNFT v1 #32349 on…
- PDB
- 2BNP
- Type
- protein
- Length
- 819 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
- P0C0Y8, P0C0Y9, P0C0Y7
- Ligands
- BCL, BPH, MST, U10, FE2, PO4, CL
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reaction center protein L chain | protein | 281 | 62% helix, 4% strand | P0C0Y8 |
| B | Reaction center protein M chain | protein | 301 | 63% helix, 4% strand | P0C0Y9 |
| C | Reaction center protein H chain | protein | 237 | 24% helix, 24% strand | P0C0Y7 |
Ligands and binding sites
- BCL · Bacteriochlorophyll A · ligand · 4 copies · chains A, B
- BPH · Bacteriopheophytin A · ligand · 2 copies · chains A, B
- MST · 2-T-butylamino-4-ethylamino-6-methylthio-S-triazine · ligand · chains A, C
- U10 · Ubiquinone-10 · ligand · chains A, B
- FE2 · Fe (II) ion · metal · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 718 | 0.81 | 0.84 | 55 | BCL |
| 2 | 251 | 0.75 | 0.88 | 47 | U10 |
| 3 | 72 | 0.71 | 0.96 | 28 | empty |
| 4 | 181 | 0.63 | 0.84 | 36 | empty |
| 5 | 143 | 0.60 | 0.84 | 26 | MST |
Interfaces
3 interfaces between chains.
- A–B · 4666 Ų buried · 72 hydrogen bonds · protein-protein
- B–C · 2904 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 1637 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 2BNP · Lipidic cubic phase grown reaction centre from Rhodobacter sphaeroides, ground state · the same entry in another collection · chain A against A, TM-score 1.00
- P0C0Y9 · AlphaFold monomer V2.0 prediction for reaction center protein M chain (P0C0Y9) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P0C0Y8 · AlphaFold monomer V2.0 prediction for reaction center protein L chain (P0C0Y8) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P0C0Y7 · AlphaFold monomer V2.0 prediction for reaction center protein H chain (P0C0Y7) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P0C0Y8
- Every structure of UniProt P0C0Y9
- Every structure of UniProt P0C0Y7
- Elsewhere: RCSB PDB 2BNP · PDBe 2BNP · UniProt P0C0Y8 · UniProt P0C0Y9 · UniProt P0C0Y7
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