Research workbench
Crystal structure of TT1020 from thermus thermophilus HB8
Analyse Crystal structure of TT1020 from thermus thermophilus HB8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1V3S
- Type
- protein
- Length
- 281 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrogen regulatory protein P-II
- UniProt
- Q5SM86
- Ligands
- ATP
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrogen regulatory protein P-II | protein | 97 | 28% helix, 39% strand | Q5SM86 |
| B | Nitrogen regulatory protein P-II | protein | 93 | 30% helix, 40% strand | Q5SM86 |
| C | Nitrogen regulatory protein P-II | protein | 91 | 31% helix, 41% strand | Q5SM86 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 344 | 0.67 | 0.81 | 42 | ATP |
| 2 | 237 | 0.63 | 0.82 | 36 | ATP |
| 3 | 249 | 0.61 | 0.80 | 36 | ATP |
| 4 | 76 | 0.41 | 0.80 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1172 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1111 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1099 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 1V3S · Crystal structure of TT1020 from Thermus thermophilus HB8 · 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 Q5SM86
- Elsewhere: RCSB PDB 1V3S · PDBe 1V3S · UniProt Q5SM86
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