MolNFT v1 · #12085 · protein + DNA
MATALPHA2 homeodomain bound to DNA
1K61 · 5'- D(*AP*CP*AP*TP*GP*TP*AP*AP*TP*TP*CP*AP*TP*TP*TP*AP*CP*AP…: “MATALPHA2 homeodomain bound to DNA”. X-ray diffraction, 5 pockets (best druggability 0.73). MolNFT v1 #12085 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1K61
- Type
- protein + DNA
- Length
- 275 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'- D(*AP*CP*AP*TP*GP*TP*AP*AP*TP*TP*CP*AP*TP*TP*TP*AP*CP*AP*CP *GP*C)-3'; 5'-D(*(5IU)…
- UniProt
- P01367
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 67% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | 5'- D(*AP*CP*AP*TP*GP*TP*AP*AP*TP*TP*CP*AP*TP*TP*TP*AP*CP*AP*CP *GP*C)-3' | dna | 21 | — | — |
| F | 5'-D(*(5IU) P*GP*CP*GP*TP*GP*TP*AP*AP*AP*TP*GP*AP*AP*TP*TP*AP*CP*AP*TP* G)-3' | dna | 21 | — | — |
| A | Mating-type protein alpha-2 | protein | 60 | 67% helix, 0% strand | P01367 |
| B | Mating-type protein alpha-2 | protein | 59 | 66% helix, 0% strand | P01367 |
| C | Mating-type protein alpha-2 | protein | 56 | 71% helix, 0% strand | P01367 |
| D | Mating-type protein alpha-2 | protein | 58 | 66% helix, 0% strand | P01367 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 249 | 0.73 | 0.88 | 27 | empty |
| 2 | 323 | 0.69 | 0.83 | 38 | empty |
| 3 | 317 | 0.59 | 0.78 | 44 | empty |
| 4 | 102 | 0.42 | 0.78 | 12 | empty |
| 5 | 92 | 0.34 | 0.75 | 16 | empty |
Interfaces
12 interfaces between chains.
- E–F · 917 Ų buried · 74 hydrogen bonds · nucleic-nucleic
- E–D · 539 Ų buried · 7 hydrogen bonds · protein-nucleic
- E–B · 451 Ų buried · 10 hydrogen bonds · protein-nucleic
- F–A · 449 Ų buried · 9 hydrogen bonds · protein-nucleic
- E–A · 447 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1K61 · MATALPHA2 homeodomain bound to DNA · the same entry in another collection · chain E against E, 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 P01367
- Elsewhere: RCSB PDB 1K61 · PDBe 1K61 · UniProt P01367
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