Research workbench
Crystal structure of rabbit NOD2 in an ADP-bound state (crystal FORM1)
Analyse Crystal structure of rabbit NOD2 in an ADP-bound state (crystal FORM1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IRN
- Type
- protein
- Length
- 746 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- G1T469
- Ligands
- ADP
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 746 | 51% helix, 11% strand | G1T469 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 554 | 0.78 | 0.85 | 74 | empty |
| 2 | 773 | 0.78 | 0.81 | 62 | ADP |
| 3 | 128 | 0.51 | 0.80 | 19 | empty |
| 4 | 171 | 0.50 | 0.77 | 21 | empty |
| 5 | 90 | 0.43 | 0.78 | 14 | empty |
Compared structures
- 5IRN · Crystal structure of rabbit NOD2 in an ADP-bound state (Crystal form1) · 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 G1T469
- Elsewhere: RCSB PDB 5IRN · PDBe 5IRN · UniProt G1T469
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