MolNFT v1 · #56113 · protein
Bacterioruberin in the trimeric structure of archaerhodopsin-2
2Z55: “Bacterioruberin in the trimeric structure of archaerhodopsin-2”. X-ray diffraction, 6 ligands (RET, 22B, L2P), 9 pockets (best druggability 0.80). MolNFT v1 #56113 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2Z55
- Type
- protein
- Length
- 955 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Archaerhodopsin-2
- UniProt
- P29563
- Ligands
- RET, 22B, L2P, GLC, MAN, GAL
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Archaerhodopsin-2 | protein | 242 | 71% helix, 3% strand | P29563 |
| B, E | Archaerhodopsin-2 | protein | 238 | 73% helix, 3% strand | P29563 |
| D | Archaerhodopsin-2 | protein | 237 | 73% helix, 2% strand | P29563 |
Ligands and binding sites
- RET · Retinal · ligand · 4 copies · chains A, B, D, E
- 22B · Bacterioruberin · ligand · 4 copies · chains A, B, D, E
- L2P · 2,3-di-phytanyl-glycerol · ligand · 4 copies · chains A, B, D, E
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, E
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B, D, E
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.80 | 0.97 | 22 | RET |
| 2 | 146 | 0.80 | 0.96 | 25 | RET |
| 3 | 129 | 0.79 | 0.96 | 20 | RET |
| 4 | 129 | 0.78 | 0.96 | 24 | RET |
| 5 | 686 | 0.73 | 0.79 | 43 | empty |
Interfaces
5 interfaces between chains.
- A–E · 351 Ų buried · 0 hydrogen bonds · protein-protein
- D–E · 348 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 346 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 294 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 19 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (retinal Schiff base).
Compared structures
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 P29563
- Elsewhere: RCSB PDB 2Z55 · PDBe 2Z55 · UniProt P29563
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