MolNFT v1 · #114013 · protein
Crystal structure of thermophilic rhodopsin.
5AZD · Bacteriorhodopsin: “Crystal structure of thermophilic rhodopsin.”. X-ray diffraction, 12 pockets (best druggability 0.86). MolNFT v1 #114013 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5AZD
- Type
- protein
- Length
- 1,002 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriorhodopsin
- UniProt
- H9ZSC3
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 82% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacteriorhodopsin | protein | 251 | 82% helix, 4% strand | H9ZSC3 |
| B | Bacteriorhodopsin | protein | 250 | 82% helix, 4% strand | H9ZSC3 |
| C | Bacteriorhodopsin | protein | 251 | 82% helix, 4% strand | H9ZSC3 |
| D | Bacteriorhodopsin | protein | 250 | 82% helix, 4% strand | H9ZSC3 |
Pockets
12 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 840 | 0.86 | 0.87 | 64 | empty |
| 2 | 912 | 0.85 | 0.86 | 88 | empty |
| 3 | 366 | 0.70 | 0.82 | 49 | empty |
| 4 | 486 | 0.66 | 0.77 | 45 | empty |
| 5 | 375 | 0.64 | 0.79 | 40 | empty |
Interfaces
5 interfaces between chains.
- A–C · 836 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 814 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 677 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 642 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 386 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 5AZD · Crystal structure of thermophilic rhodopsin. · the same entry in another collection · chain B against B, 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 H9ZSC3
- Elsewhere: RCSB PDB 5AZD · PDBe 5AZD · UniProt H9ZSC3
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