Research workbench
NOD1 card domain with three disulfide-clinched, domain-swapped dimers in the asymmetric unit
Analyse NOD1 card domain with three disulfide-clinched, domain-swapped dimers in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4E9M
- Type
- protein
- Length
- 559 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleotide-binding oligomerization domain-containing protein 1
- UniProt
- Q9Y239
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleotide-binding oligomerization domain-containing protein 1 | protein | 97 | 75% helix, 0% strand | Q9Y239 |
| B, D | Nucleotide-binding oligomerization domain-containing protein 1 | protein | 95 | 77% helix, 0% strand | Q9Y239 |
| C | Nucleotide-binding oligomerization domain-containing protein 1 | protein | 91 | 75% helix, 0% strand | Q9Y239 |
| E | Nucleotide-binding oligomerization domain-containing protein 1 | protein | 87 | 72% helix, 0% strand | Q9Y239 |
| F | Nucleotide-binding oligomerization domain-containing protein 1 | protein | 94 | 68% helix, 0% strand | Q9Y239 |
Ligands and binding sites
- FLC · Citrate anion · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.77 | 0.97 | 34 | empty |
| 2 | 103 | 0.75 | 0.96 | 39 | empty |
| 3 | 150 | 0.46 | 0.77 | 36 | empty |
| 4 | 111 | 0.46 | 0.79 | 21 | empty |
| 5 | 56 | 0.45 | 0.84 | 18 | empty |
Interfaces
11 interfaces between chains.
- A–B · 1693 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1596 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1484 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 565 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 525 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4E9M · NOD1 card domain with three disulfide-clinched, domain-swapped dimers in the asymmetric… · the same entry in another collection · chain F against F, TM-score 1.00
- Q9Y239 · AlphaFold monomer V2.0 prediction for nucleotide-binding oligomerization… · a predicted model of the same protein · chain E against A, TM-score 0.90
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 Q9Y239
- Elsewhere: RCSB PDB 4E9M · PDBe 4E9M · UniProt Q9Y239
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