Research workbench
NMR structure of the homeodomain of PITX2 in complex with a taatcc DNA binding site
Analyse NMR structure of the homeodomain of PITX2 in complex with a taatcc DNA binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2LKX
- Type
- protein + DNA
- Length
- 94 residues
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pituitary homeobox 3; DNA (5'-D(*GP*CP*TP*CP*TP*AP*AP*TP*CP*CP*CP*CP*G)-3'); DNA…
- UniProt
- O75364
- Pockets
- 2 · best druggability 0.41
Structure
solution nmr · 3 distinct chains · 60% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pituitary homeobox 3 | protein | 68 | 60% helix, 0% strand | O75364 |
| B | DNA (5'-D(*GP*CP*TP*CP*TP*AP*AP*TP*CP*CP*CP*CP*G)-3') | dna | 13 | — | — |
| C | DNA (5'-D(*CP*GP*GP*GP*GP*AP*TP*TP*AP*GP*AP*GP*C)-3') | dna | 13 | — | — |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.41 | 0.74 | 22 | empty |
| 2 | 78 | 0.29 | 0.73 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–C · 754 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–B · 629 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–C · 575 Ų buried · 46 hydrogen bonds · nucleic-nucleic
Compared structures
- 2LKX · NMR structure of the homeodomain of Pitx2 in complex with a TAATCC DNA binding site · the same entry in another collection · chain A against A, TM-score 1.00
- O75364 · AlphaFold monomer V2.0 prediction for pituitary homeobox 3 (O75364) · a predicted model of the same protein · chain A against A, TM-score 0.79
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 O75364
- Elsewhere: RCSB PDB 2LKX · PDBe 2LKX · UniProt O75364
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