Research workbench
Thermus thermophilus pilb core ATPase region
Analyse Thermus thermophilus pilb core ATPase region in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IT5
- Type
- protein
- Length
- 2,310 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP binding motif-containing protein pilf
- UniProt
- Q8VRL1
- Ligands
- AGS, ATP, ZN, MG
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F, A, B, E, C, D | ATP binding motif-containing protein pilf | protein | 385 | 36% helix, 30% strand | Q8VRL1 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 5 copies · chains A, B, E, C, D
- ATP · Adenosine-5'-triphosphate · ligand · chains F
- ZN · Zinc ion · metal · 6 copies · chains F, A, B, E, C, D
- MG · Magnesium ion · metal · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1062 | 0.85 | 0.86 | 94 | ATP |
| 2 | 988 | 0.84 | 0.85 | 103 | AGS |
| 3 | 961 | 0.84 | 0.85 | 101 | AGS |
| 4 | 1131 | 0.82 | 0.83 | 84 | AGS |
| 5 | 829 | 0.82 | 0.84 | 85 | AGS, MG |
Interfaces
6 interfaces between chains.
- B–C · 1741 Ų buried · 30 hydrogen bonds · protein-protein
- F–E · 1697 Ų buried · 32 hydrogen bonds · protein-protein
- F–A · 1623 Ų buried · 31 hydrogen bonds · protein-protein
- E–D · 1614 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 1551 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5IT5 · Thermus thermophilus PilB core ATPase region · the same entry in another collection · chain F against F, 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 Q8VRL1
- Elsewhere: RCSB PDB 5IT5 · PDBe 5IT5 · UniProt Q8VRL1
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