Research workbench
Crystal structure of the MATA1/MATALPHA2 homeodomain heterodimer bound to DNA
Analyse Crystal structure of the MATA1/MATALPHA2 homeodomain heterodimer bound to DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YRN
- Type
- protein + DNA
- Length
- 169 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*TP*AP*CP*AP*TP*GP*TP*AP*AP*TP*TP*TP*AP*TP*TP*AP*C P*AP*TP*CP*A)-3'); DNA (5'…
- UniProt
- P01366, Q6B2C0
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 65% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'- D(*TP*AP*CP*AP*TP*GP*TP*AP*AP*TP*TP*TP*AP*TP*TP*AP*C P*AP*TP*CP*A)-3') | dna | 21 | — | — |
| D | DNA (5'- D(*TP*AP*TP*GP*AP*TP*GP*TP*AP*AP*TP*AP*AP*AP*TP*TP*A P*CP*AP*TP*G)-3') | dna | 21 | — | — |
| A | Protein (mat A1 homeodomain) | protein | 49 | 76% helix, 0% strand | P01366 |
| B | Protein (mat ALPHA2 homeodomain) | protein | 78 | 59% helix, 0% strand | Q6B2C0 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.60 | 0.77 | 37 | empty |
| 2 | 70 | 0.45 | 0.82 | 14 | empty |
| 3 | 103 | 0.40 | 0.77 | 17 | empty |
Interfaces
6 interfaces between chains.
- C–D · 873 Ų buried · 94 hydrogen bonds · nucleic-nucleic
- A–B · 658 Ų buried · 6 hydrogen bonds · protein-protein
- C–B · 624 Ų buried · 12 hydrogen bonds · protein-nucleic
- D–B · 548 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–A · 394 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 1YRN · Crystal structure of the MATA1/MATALPHA2 homeodomain heterodimer bound to DNA · the same entry in another collection · chain C against C, TM-score 1.00
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 P01366
- Every structure of UniProt Q6B2C0
- Elsewhere: RCSB PDB 1YRN · PDBe 1YRN · UniProt P01366 · UniProt Q6B2C0
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