Research workbench
Crystal structure of human NLRP12-pyd with a mbp tag
Analyse Crystal structure of human NLRP12-pyd with a mbp tag in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H7N
- Type
- protein
- Length
- 917 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NLRP12-pyd with mbp tag
- Ligands
- GLC, SO4
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NLRP12-pyd with mbp tag | protein | 457 | 51% helix, 17% strand | — |
| B | NLRP12-pyd with mbp tag | protein | 460 | 51% helix, 18% strand | — |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 8 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1023 | 0.81 | 0.82 | 126 | GLC, EDO |
| 2 | 400 | 0.72 | 0.83 | 36 | GLC |
| 3 | 618 | 0.68 | 0.77 | 52 | empty |
| 4 | 261 | 0.55 | 0.77 | 28 | empty |
| 5 | 59 | 0.41 | 0.81 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 708 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5H7N · Crystal structure of human NLRP12-PYD with a MBP tag · 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
- Elsewhere: RCSB PDB 5H7N · PDBe 5H7N
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