MolNFT v1 · #12123 · protein + DNA
PAX5(1-149)+ETS-1(331-440)+DNA
1K78 · PAX5/ETS binding site on the mb-1 promoter: “PAX5(1-149)+ETS-1(331-440)+DNA”. X-ray diffraction, 15 pockets (best druggability 0.72). MolNFT v1 #12123 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1K78
- Type
- protein + DNA
- Length
- 619 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PAX5/ETS binding site on the mb-1 promoter; Paired box protein PAX5; C-ets-1 protein
- UniProt
- Q02548, P27577
- Pockets
- 15 · best druggability 0.72
Structure
x-ray diffraction · 6 distinct chains · 51% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, G | PAX5/ETS binding site on the mb-1 promoter | dna | 27 | — | — |
| D, H | PAX5/ETS binding site on the mb-1 promoter | dna | 27 | — | — |
| A, E | Paired box protein PAX5 | protein | 124 | 53% helix, 2% strand | Q02548 |
| B | C-ets-1 protein | protein | 102 | 49% helix, 12% strand | P27577 |
| F | C-ets-1 protein | protein | 103 | 49% helix, 12% strand | P27577 |
| I | Paired box protein PAX5 | protein | 58 | 55% helix, 0% strand | Q02548 |
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.72 | 0.94 | 23 | empty |
| 2 | 137 | 0.72 | 0.92 | 33 | empty |
| 3 | 266 | 0.62 | 0.81 | 23 | empty |
| 4 | 208 | 0.59 | 0.81 | 27 | empty |
| 5 | 160 | 0.53 | 0.80 | 22 | empty |
Interfaces
21 interfaces between chains.
- G–H · 1137 Ų buried · 96 hydrogen bonds · nucleic-nucleic
- C–D · 1129 Ų buried · 94 hydrogen bonds · nucleic-nucleic
- D–A · 1039 Ų buried · 20 hydrogen bonds · protein-nucleic
- H–E · 1006 Ų buried · 17 hydrogen bonds · protein-nucleic
- G–E · 960 Ų buried · 24 hydrogen bonds · protein-nucleic
Compared structures
- 1K78 · Pax5(1-149)+Ets-1(331-440)+DNA · the same entry in another collection · chain I against I, TM-score 1.00
- P27577 · AlphaFold monomer V2.0 prediction for protein C-ets-1 (P27577) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q02548 · AlphaFold monomer V2.0 prediction for paired box protein pax-5 (Q02548) · a predicted model of the same protein · chain I 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 Q02548
- Every structure of UniProt P27577
- Elsewhere: RCSB PDB 1K78 · PDBe 1K78 · UniProt Q02548 · UniProt P27577
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