MolNFT v1 · #116946 · protein
Crystal structure of MUPP1 PDZ8 domain from rattus norvegicus
5DTH · Multiple PDZ domain protein: “Crystal structure of MUPP1 PDZ8 domain from rattus norvegicus”. X-ray diffraction, 3 pockets (best druggability 0.72). MolNFT v1 #116946 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DTH
- Type
- protein
- Length
- 428 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Multiple PDZ domain protein
- UniProt
- O55164
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Multiple PDZ domain protein | protein | 106 | 22% helix, 32% strand | O55164 |
| B | Multiple PDZ domain protein | protein | 109 | 21% helix, 31% strand | O55164 |
| C | Multiple PDZ domain protein | protein | 107 | 21% helix, 36% strand | O55164 |
| D | Multiple PDZ domain protein | protein | 106 | 25% helix, 38% strand | O55164 |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 582 | 0.72 | 0.80 | 70 | empty |
| 2 | 636 | 0.71 | 0.79 | 48 | empty |
| 3 | 63 | 0.31 | 0.75 | 15 | empty |
Interfaces
5 interfaces between chains.
- B–D · 582 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 475 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 400 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 376 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 82 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5DTH · Crystal structure of MUPP1 PDZ8 domain from rattus norvegicus · the same entry in another collection · chain D against D, TM-score 1.00
- O55164 · AlphaFold monomer V2.0 prediction for multiple PDZ domain protein (O55164) · a predicted model of the same protein · chain D against A, TM-score 0.93
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 O55164
- Elsewhere: RCSB PDB 5DTH · PDBe 5DTH · UniProt O55164
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