MolNFT v1 · #109947 · protein
Crystal structure of human NLRP12 pyd domain and implication in homotypic interaction
4XHS · Maltose-binding periplasmic PROTEIN,NACHT, lrr and pyd…: “Crystal structure of human NLRP12 pyd domain and implication in homotypic interaction”. X-ray diffraction, 2 ligands (GLC, NA), 12 pockets (best druggability 0.72). MolNFT v1…
- 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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