MolNFT v1 · #139148 · protein + DNA
Crystal structure of SMAD5-MH1/PALINDROMIC sbe DNA complex
5X6G · Mothers against decapentaplegic homolog 5: “Crystal structure of SMAD5-MH1/PALINDROMIC sbe DNA complex”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.65). MolNFT v1 #139148 on GenesisL1: 3D structure, binding…
- PDB
- 5X6G
- Type
- protein + DNA
- Length
- 275 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mothers against decapentaplegic homolog 5; DNA…
- UniProt
- P97454
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mothers against decapentaplegic homolog 5 | protein | 122 | 46% helix, 15% strand | P97454 |
| B | Mothers against decapentaplegic homolog 5 | protein | 123 | 42% helix, 15% strand | P97454 |
| C | DNA (5'-D(P*AP*TP*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*AP*TP*A)- 3') | dna | 15 | — | — |
| D | DNA (5'-D(P*GP*TP*AP*TP*GP*TP*CP*TP*AP*GP*AP*CP*TP*GP*A)- 3') | dna | 15 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 617 | 0.65 | 0.76 | 48 | empty |
| 2 | 209 | 0.51 | 0.77 | 29 | empty |
| 3 | 147 | 0.46 | 0.77 | 20 | empty |
Interfaces
6 interfaces between chains.
- C–D · 695 Ų buried · 56 hydrogen bonds · nucleic-nucleic
- B–D · 353 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–C · 327 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–D · 230 Ų buried · 3 hydrogen bonds · protein-nucleic
- B–C · 219 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 5X6G · Crystal Structure of SMAD5-MH1/palindromic SBE DNA complex · the same entry in another collection · chain A against A, TM-score 1.00
- P97454 · AlphaFold monomer V2.0 prediction for mothers against decapentaplegic homolog 5 (P97454) · a predicted model of the same protein · chain A against A, TM-score 0.85
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 P97454
- Elsewhere: RCSB PDB 5X6G · PDBe 5X6G · UniProt P97454
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