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Crystal structure of an ABC transporter ATP-binding protein (TM_1403) from Thermotoga maritima MSB8 at 2.35 A resolution
Analyse Crystal structure of an ABC transporter ATP-binding protein (TM_1403) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YER
- Type
- protein
- Length
- 562 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.35
- Source
- Thermotoga maritima
- Molecule
- ABC transporter ATP-binding protein
- UniProt
- Q9X1C3
- Ligands
- ADP, CL
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · resolution 2.35 · 2 distinct chains · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ABC transporter ATP-binding protein | protein | 285 | 34% helix, 30% strand | Q9X1C3 |
| B | ABC transporter ATP-binding protein | protein | 277 | 35% helix, 28% strand | Q9X1C3 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 828 | 0.78 | 0.81 | 58 | CL |
| 2 | 1082 | 0.77 | 0.79 | 84 | ADP |
| 3 | 130 | 0.42 | 0.75 | 25 | empty |
| 4 | 70 | 0.38 | 0.78 | 18 | empty |
| 5 | 85 | 0.34 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1073 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 4YER · Crystal structure of an ABC transporter ATP-binding protein (TM_1403) from thermotoga… · 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 Q9X1C3
- Elsewhere: RCSB PDB 4YER · PDBe 4YER · UniProt Q9X1C3
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