MolNFT v1 · #126839 · protein + DNA
Crystal structure of SMAD4-MH1 bound to the ggct site.
5MEZ · MH1 domain of human SMAD4: “Crystal structure of SMAD4-MH1 bound to the ggct site.”. X-ray diffraction, 2 ligands (ZN, CL), 4 pockets (best druggability 0.56). MolNFT v1 #126839 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5MEZ
- Type
- protein + DNA
- Length
- 277 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MH1 domain of human SMAD4; DNA (5'-D(P*GP*CP*AP*GP*GP*CP*TP*AP*GP*CP*CP*TP*GP*CP*A)- 3')
- UniProt
- Q13485
- Ligands
- ZN, CL
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MH1 domain of human SMAD4 | protein | 125 | 38% helix, 14% strand | Q13485 |
| B | MH1 domain of human SMAD4 | protein | 122 | 42% helix, 15% strand | Q13485 |
| D, E | DNA (5'-D(P*GP*CP*AP*GP*GP*CP*TP*AP*GP*CP*CP*TP*GP*CP*A)- 3') | dna | 15 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 381 | 0.56 | 0.75 | 30 | empty |
| 2 | 113 | 0.46 | 0.79 | 20 | empty |
| 3 | 114 | 0.39 | 0.75 | 27 | empty |
| 4 | 63 | 0.29 | 0.74 | 14 | empty |
Interfaces
4 interfaces between chains.
- D–E · 697 Ų buried · 82 hydrogen bonds · nucleic-nucleic
- A–B · 543 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 384 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–E · 165 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 5MEZ · Crystal structure of Smad4-MH1 bound to the GGCT site. · the same entry in another collection · chain D against D, TM-score 1.00
- Q13485 · AlphaFold monomer V2.0 prediction for mothers against decapentaplegic homolog 4 (Q13485) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q13485
- Elsewhere: RCSB PDB 5MEZ · PDBe 5MEZ · UniProt Q13485
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.