MolNFT v1 · #25427 · protein
Crystal structure of oligopeptide ABC transporter, periplasmic oligopeptide-binding (TM1223) from thermotoga maritima at 1.73 a resolution
1VR5 · Oligopeptide ABC transporter, periplasmic oligopeptide…: “Crystal structure of oligopeptide ABC transporter, periplasmic oligopeptide-binding (TM1223) from thermotoga…”. X-ray diffraction, 2 ligands (NA, CL), 4 pockets (best…
- PDB
- 1VR5
- Type
- protein
- Length
- 1,072 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oligopeptide ABC transporter, periplasmic oligopeptide- binding protein
- UniProt
- Q9X0V0
- Ligands
- NA, CL
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Oligopeptide ABC transporter, periplasmic oligopeptide- binding protein | protein | 536 | 33% helix, 21% strand | Q9X0V0 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 30 copies · chains A, B
- ACT · Acetate ion · additive · 4 copies · chains A, B
- FMT · Formic acid · additive · 2 copies · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 879 | 0.78 | 0.81 | 71 | ACT, EDO |
| 2 | 1200 | 0.77 | 0.79 | 84 | ACT, EDO |
| 3 | 115 | 0.44 | 0.77 | 25 | EDO |
| 4 | 121 | 0.43 | 0.77 | 27 | EDO |
Interfaces
1 interface between chains.
- A–B · 324 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 1VR5 · Crystal structure of Oligopeptide ABC transporter, periplasmic oligopeptide-binding… · 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 Q9X0V0
- Elsewhere: RCSB PDB 1VR5 · PDBe 1VR5 · UniProt Q9X0V0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.