Research workbench
TBX5 db, NKX2.5 hd, anf DNA complex
Analyse TBX5 db, NKX2.5 hd, anf DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4S0H
- Type
- protein + DNA
- Length
- 535 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-box transcription factor TBX5; Homeobox protein nkx-2.5…
- UniProt
- Q99593, P52952
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 25% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T-box transcription factor TBX5 | protein | 176 | 19% helix, 39% strand | Q99593 |
| B, F | Homeobox protein nkx-2.5 | protein | 53 | 68% helix, 0% strand | P52952 |
| E | T-box transcription factor TBX5 | protein | 177 | 19% helix, 37% strand | Q99593 |
| C, G | 5'-D(*TP*CP*TP*CP*AP*CP*AP*CP*CP*TP*TP*TP*GP*AP*AP*GP*TP*GP *G)-3' | dna | 19 | — | — |
| D, H | 5'-D(*CP*CP*AP*CP*TP*TP*CP*AP*AP*AP*GP*GP*TP*GP*TP*GP*AP*GP *a)-3' | dna | 19 | — | — |
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 680 | 0.77 | 0.82 | 71 | empty |
| 2 | 216 | 0.72 | 0.88 | 39 | empty |
| 3 | 291 | 0.64 | 0.81 | 39 | empty |
| 4 | 201 | 0.61 | 0.83 | 21 | empty |
| 5 | 288 | 0.60 | 0.79 | 32 | empty |
Interfaces
15 interfaces between chains.
- G–H · 857 Ų buried · 90 hydrogen bonds · nucleic-nucleic
- C–D · 848 Ų buried · 88 hydrogen bonds · nucleic-nucleic
- A–E · 825 Ų buried · 8 hydrogen bonds · protein-protein
- E–H · 525 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–D · 523 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 4S0H · TBX5 DB, NKX2.5 HD, ANF DNA Complex · the same entry in another collection · chain H against H, TM-score 1.00
- Q99593 · AlphaFold monomer V2.0 prediction for T-box transcription factor TBX5 (Q99593) · a predicted model of the same protein · chain E against A, TM-score 0.98
- P52952 · AlphaFold monomer V2.0 prediction for homeobox protein nkx-2.5 (P52952) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q99593
- Every structure of UniProt P52952
- Elsewhere: RCSB PDB 4S0H · PDBe 4S0H · UniProt Q99593 · UniProt P52952
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