MolNFT v1 · #8695 · protein + DNA
Crystal structure of ternary protein-DNA COMPLEX2
1H89 · CAAT/ENHANCER binding protein beta: “Crystal structure of ternary protein-DNA COMPLEX2”. X-ray diffraction, 1 ligand (K), 7 pockets (best druggability 0.73). MolNFT v1 #8695 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1H89
- Type
- protein + DNA
- Length
- 295 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CAAT/ENHANCER binding protein beta; Myb proto-oncogene protein…
- UniProt
- P17676
- Ligands
- K
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | CAAT/ENHANCER binding protein beta | protein | 64 | 92% helix, 0% strand | P17676 |
| C | Myb proto-oncogene protein | protein | 115 | 63% helix, 0% strand | — |
| 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
- K · Potassium ion · metal · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 572 | 0.73 | 0.81 | 32 | empty |
| 2 | 486 | 0.67 | 0.79 | 36 | empty |
| 3 | 157 | 0.53 | 0.80 | 25 | K |
| 4 | 88 | 0.52 | 0.84 | 19 | empty |
| 5 | 166 | 0.50 | 0.78 | 16 | empty |
Interfaces
8 interfaces between chains.
- D–E · 1116 Ų buried · 91 hydrogen bonds · nucleic-nucleic
- A–B · 1108 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 623 Ų buried · 16 hydrogen bonds · protein-nucleic
- C–E · 607 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–D · 379 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
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
- Elsewhere: RCSB PDB 1H89 · PDBe 1H89 · UniProt P17676
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