Research workbench
Crystal structure of a bacteria tir domain, pdtir from paracoccus denitrificans
Analyse Crystal structure of a bacteria tir domain, pdtir from paracoccus denitrificans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H16
- Type
- protein
- Length
- 530 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tir protein
- UniProt
- A1AY86
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tir protein | protein | 136 | 41% helix, 21% strand | A1AY86 |
| B | Tir protein | protein | 137 | 49% helix, 21% strand | A1AY86 |
| C | Tir protein | protein | 127 | 47% helix, 20% strand | A1AY86 |
| D | Tir protein | protein | 130 | 44% helix, 21% strand | A1AY86 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 954 | 0.78 | 0.80 | 85 | empty |
| 2 | 188 | 0.50 | 0.77 | 24 | empty |
| 3 | 65 | 0.31 | 0.75 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–B · 810 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 675 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 644 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 243 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 65 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3H16 · Crystal structure of a bacteria TIR domain, PdTIR from Paracoccus denitrificans · the same entry in another collection · chain D against D, TM-score 1.00
- A1AY86 · AlphaFold monomer V2.0 prediction for NAD(+) hydrolase pdtir (A1AY86) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 A1AY86
- Elsewhere: RCSB PDB 3H16 · PDBe 3H16 · UniProt A1AY86
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