Research workbench
Crystal structure of NKX2-5 and TBX5 bound to the nppa promoter region
Analyse Crystal structure of NKX2-5 and TBX5 bound to the nppa promoter region in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FLV
- Type
- protein + DNA
- Length
- 1,077 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homeobox protein nkx-2.5, T-box transcription factor TBX5…
- UniProt
- P42582, P70326
- Pockets
- 18 · best druggability 0.76
Structure
x-ray diffraction · 8 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homeobox protein nkx-2.5, T-box transcription factor TBX5 | protein | 226 | 28% helix, 30% strand | P42582, P70326 |
| B, F, J, N | 5'-D(*TP*CP*TP*TP*CP*TP*CP*AP*CP*AP*CP*CP*TP*TP *TP*GP*AP*AP*GP*TP*GP*G)-3' | dna | 21 | — | — |
| C | 5'-D(*AP*CP*CP*AP*CP*TP*TP*CP*AP*AP*AP*GP*GP*TP *GP*TP*GP*AP*GP*AP*AP*G)-3' | dna | 20 | — | — |
| E | Homeobox protein nkx-2.5, T-box transcription factor TBX5 | protein | 227 | 31% helix, 29% strand | P42582, P70326 |
| G | 5'-D(*AP*CP*CP*AP*CP*TP*TP*CP*AP*AP*AP*GP*GP*TP *GP*TP*GP*AP*GP*AP*AP*G)-3' | dna | 21 | — | — |
| I | Homeobox protein nkx-2.5, T-box transcription factor TBX5 | protein | 226 | 30% helix, 24% strand | P42582, P70326 |
| K, O | 5'-D(*AP*CP*CP*AP*CP*TP*TP*CP*AP*AP*AP*GP*GP*TP *GP*TP*GP*AP*GP*AP*AP*G)-3' | dna | 22 | — | — |
| M | Homeobox protein nkx-2.5, T-box transcription factor TBX5 | protein | 229 | 29% helix, 30% strand | P42582, P70326 |
Ligands and binding sites
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, O, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 619 | 0.76 | 0.82 | 80 | empty |
| 2 | 721 | 0.74 | 0.80 | 67 | empty |
| 3 | 872 | 0.74 | 0.78 | 62 | PG4 |
| 4 | 527 | 0.73 | 0.82 | 68 | empty |
| 5 | 574 | 0.73 | 0.81 | 65 | empty |
Interfaces
23 interfaces between chains.
- A–E · 1197 Ų buried · 10 hydrogen bonds · protein-protein
- I–K · 1073 Ų buried · 14 hydrogen bonds · protein-nucleic
- I–J · 939 Ų buried · 8 hydrogen bonds · protein-nucleic
- N–O · 937 Ų buried · 90 hydrogen bonds · nucleic-nucleic
- M–N · 937 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 5FLV · Crystal structure of NKX2-5 and TBX5 bound to the Nppa promoter region · the same entry in another collection · chain O against O, 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 P42582
- Every structure of UniProt P70326
- Elsewhere: RCSB PDB 5FLV · PDBe 5FLV · UniProt P42582 · UniProt P70326
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