Research workbench
Crystal structure of ternary protein-DNA COMPLEX1
Analyse Crystal structure of ternary protein-DNA COMPLEX1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1H88
- Type
- protein + DNA
- Length
- 345 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CCAAT/ENHANCER binding protein beta; Myb proto-oncogene protein…
- UniProt
- P17676, P06876
- Ligands
- NH4
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CCAAT/ENHANCER binding protein beta | protein | 70 | 87% helix, 0% strand | P17676 |
| B | CCAAT/ENHANCER binding protein beta | protein | 71 | 86% helix, 0% strand | P17676 |
| C | Myb proto-oncogene protein | protein | 152 | 63% helix, 0% strand | P06876 |
| D | DNA(5'-(*GP*AP*TP*GP*TP*GP*GP*CP*GP*CP*AP* AP*TP*CP*CP*TP*TP*AP*AP*CP*GP*GP*AP*CP*TP*G)-3') | dna | 26 | — | — |
| E | DNA(5'-(*CP*CP*AP*GP*TP*CP*CP*GP*TP*TP*AP* AP*GP*GP*AP*TP*TP*GP*CP*GP*CP*CP*AP*CP*AP*T)-3') | dna | 26 | — | — |
Ligands and binding sites
- NH4 · Ammonium ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.74 | 0.82 | 35 | empty |
| 2 | 759 | 0.70 | 0.77 | 61 | NH4 |
| 3 | 185 | 0.49 | 0.77 | 18 | empty |
| 4 | 133 | 0.45 | 0.77 | 16 | empty |
| 5 | 112 | 0.41 | 0.76 | 18 | empty |
Interfaces
8 interfaces between chains.
- D–E · 1122 Ų buried · 92 hydrogen bonds · nucleic-nucleic
- A–B · 1044 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 591 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–D · 542 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–D · 393 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 1H88 · Crystal structure of ternary protein-DNA COMPLEX1 · the same entry in another collection · chain E against E, TM-score 1.00
- P06876 · AlphaFold monomer V2.0 prediction for transcriptional activator myb (P06876) · a predicted model of the same protein · chain C against A, TM-score 0.92
- P17676 · AlphaFold monomer V2.0 prediction for CCAAT/ENHANCER-binding protein beta (P17676) · a predicted model of the same protein · chain B against A, TM-score 0.84
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 P17676
- Every structure of UniProt P06876
- Elsewhere: RCSB PDB 1H88 · PDBe 1H88 · UniProt P17676 · UniProt P06876
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