MolNFT v1 · #139154 · protein + DNA
Crystal structure of SMAD5-MH1 in complex with a composite DNA sequence
5X6M · Mothers against decapentaplegic homolog 5: “Crystal structure of SMAD5-MH1 in complex with a composite DNA sequence”. X-ray diffraction, 1 ligand (ZN), 12 pockets (best druggability 0.58). MolNFT v1 #139154 on GenesisL1: 3D…
- PDB
- 5X6M
- Type
- protein + DNA
- Length
- 574 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mothers against decapentaplegic homolog 5; DNA (5'…
- UniProt
- P97454
- Ligands
- ZN
- Pockets
- 12 · best druggability 0.58
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Mothers against decapentaplegic homolog 5 | protein | 122 | 38% helix, 13% strand | P97454 |
| C, G | DNA (5'- D(P*AP*TP*CP*AP*GP*AP*CP*TP*GP*CP*CP*GP*GP*CP*AP*GP*TP*CP*TP*AP*TP*A) -3') | dna | 22 | — | — |
| D, H | DNA (5'- D(P*TP*TP*AP*TP*AP*GP*AP*CP*TP*GP*CP*CP*GP*GP*CP*AP*GP*TP*CP*TP*GP*A) -3') | dna | 22 | — | — |
| A | Mothers against decapentaplegic homolog 5 | protein | 122 | 40% helix, 15% strand | P97454 |
| E, F | Mothers against decapentaplegic homolog 5 | protein | 121 | 41% helix, 15% strand | P97454 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains B, A, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.58 | 0.77 | 39 | empty |
| 2 | 251 | 0.54 | 0.77 | 31 | empty |
| 3 | 271 | 0.52 | 0.75 | 26 | empty |
| 4 | 54 | 0.51 | 0.87 | 13 | empty |
| 5 | 251 | 0.51 | 0.75 | 22 | empty |
Interfaces
12 interfaces between chains.
- A–F · 1111 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 1086 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 964 Ų buried · 96 hydrogen bonds · nucleic-nucleic
- G–H · 963 Ų buried · 104 hydrogen bonds · nucleic-nucleic
- C–A · 391 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 5X6M · Crystal Structure of SMAD5-MH1 in complex with a composite DNA sequence · the same entry in another collection · chain G against G, 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 E against A, TM-score 0.86
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 5X6M · PDBe 5X6M · UniProt P97454
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