Research workbench
Crystal structure of human NLRP12 pyd domain and implication in homotypic interaction
Analyse Crystal structure of human NLRP12 pyd domain and implication in homotypic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XHS
- Type
- protein
- Length
- 906 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose-binding periplasmic PROTEIN,NACHT, lrr and pyd domains-containing protein 12
- UniProt
- P0AEY0, P59046
- Ligands
- GLC, NA
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltose-binding periplasmic PROTEIN,NACHT, lrr and pyd domains-containing protein 12 | protein | 452 | 51% helix, 17% strand | P0AEY0, P59046 |
| B | Maltose-binding periplasmic PROTEIN,NACHT, lrr and pyd domains-containing protein 12 | protein | 454 | 51% helix, 17% strand | P0AEY0, P59046 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
- NA · Sodium ion · metal · 7 copies · chains A, B
- FMT · Formic acid · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 287 | 0.72 | 0.86 | 28 | GLC, FMT, NA |
| 2 | 642 | 0.71 | 0.78 | 66 | empty |
| 3 | 321 | 0.70 | 0.83 | 31 | GLC, NA |
| 4 | 279 | 0.57 | 0.77 | 35 | empty |
| 5 | 215 | 0.49 | 0.75 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 656 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4XHS · Crystal structure of human NLRP12 PYD domain and implication in homotypic interaction · the same entry in another collection · chain A against A, TM-score 1.00
- P59046 · AlphaFold monomer V2.0 prediction for nacht, lrr and pyd domains- containing protein 12… · a predicted model of the same protein · chain A against A, TM-score 0.30
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 P0AEY0
- Every structure of UniProt P59046
- Elsewhere: RCSB PDB 4XHS · PDBe 4XHS · UniProt P0AEY0 · UniProt P59046
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