MolNFT v1 · #157880 · protein
Crystal structure of human NLRP6 pyd domain with mbp fusion
6NDJ · MALTOSE/MALTODEXTRIN-binding periplasmic protein, nacht…: “Crystal structure of human NLRP6 pyd domain with mbp fusion”. X-ray diffraction, 7 pockets (best druggability 0.56). MolNFT v1 #157880 on GenesisL1: 3D structure, binding…
- PDB
- 6NDJ
- Type
- protein
- Length
- 882 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MALTOSE/MALTODEXTRIN-binding periplasmic protein, nacht, lrr and pyd domains-containing…
- UniProt
- P0AEX9, P59044
- Pockets
- 7 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MALTOSE/MALTODEXTRIN-binding periplasmic protein, nacht, lrr and pyd domains-containing protein 6 chimera | protein | 439 | 50% helix, 18% strand | P0AEX9, P59044 |
| B | MALTOSE/MALTODEXTRIN-binding periplasmic protein, nacht, lrr and pyd domains-containing protein 6 chimera | protein | 443 | 51% helix, 17% strand | P0AEX9, P59044 |
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 284 | 0.56 | 0.76 | 42 | empty |
| 2 | 294 | 0.54 | 0.75 | 47 | empty |
| 3 | 315 | 0.54 | 0.74 | 43 | empty |
| 4 | 91 | 0.50 | 0.82 | 23 | empty |
| 5 | 93 | 0.48 | 0.81 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 334 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6NDJ · Crystal structure of human NLRP6 PYD domain with MBP fusion · the same entry in another collection · chain A against A, TM-score 1.00
- P59044 · AlphaFold monomer V2.0 prediction for nacht, lrr and pyd domains- containing protein 6… · 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 P0AEX9
- Every structure of UniProt P59044
- Elsewhere: RCSB PDB 6NDJ · PDBe 6NDJ · UniProt P0AEX9 · UniProt P59044
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