Research workbench
Crystal structure of a glycerol uptake operon antiterminator-related protein (TM1436) from thermotoga maritima MSB8 at 1.65 a resolution
Analyse Crystal structure of a glycerol uptake operon antiterminator-related protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VKF
- Type
- protein
- Length
- 690 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol uptake operon antiterminator-related protein
- UniProt
- Q9X1F0
- Ligands
- PO4
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Glycerol uptake operon antiterminator-related protein | protein | 172 | 38% helix, 25% strand | Q9X1F0 |
| B, C | Glycerol uptake operon antiterminator-related protein | protein | 173 | 37% helix, 25% strand | Q9X1F0 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 207 | 0.59 | 0.80 | 38 | PO4 |
| 2 | 208 | 0.58 | 0.79 | 36 | CIT |
| 3 | 228 | 0.52 | 0.76 | 26 | empty |
| 4 | 57 | 0.35 | 0.78 | 13 | CIT |
| 5 | 74 | 0.34 | 0.75 | 16 | CIT |
Interfaces
3 interfaces between chains.
- A–B · 902 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 386 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 155 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 1VKF · Crystal structure of a glycerol uptake operon antiterminator-related protein (TM1436)… · 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 Q9X1F0
- Elsewhere: RCSB PDB 1VKF · PDBe 1VKF · UniProt Q9X1F0
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