Research workbench
Crystal structure of myc-max recognizing DNA
Analyse Crystal structure of myc-max recognizing DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NKP
- Type
- protein + DNA
- Length
- 411 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP *C)-3'; Myc proto-oncogene…
- UniProt
- P01106, P61244
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 83% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F, G, H, J | 5'-D(*CP*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP *C)-3' | dna | 19 | — | — |
| A | Myc proto-oncogene protein | protein | 88 | 84% helix, 0% strand | P01106 |
| B | Max protein | protein | 83 | 82% helix, 0% strand | P61244 |
| D | Myc proto-oncogene protein | protein | 83 | 86% helix, 0% strand | P01106 |
| E | Max protein | protein | 81 | 81% helix, 0% strand | P61244 |
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.82 | 0.96 | 23 | empty |
| 2 | 215 | 0.80 | 0.94 | 26 | empty |
| 3 | 396 | 0.62 | 0.77 | 42 | empty |
| 4 | 246 | 0.54 | 0.77 | 26 | empty |
| 5 | 176 | 0.49 | 0.77 | 22 | empty |
Interfaces
16 interfaces between chains.
- A–B · 1729 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1665 Ų buried · 12 hydrogen bonds · protein-protein
- F–G · 812 Ų buried · 70 hydrogen bonds · nucleic-nucleic
- H–J · 801 Ų buried · 72 hydrogen bonds · nucleic-nucleic
- G–A · 515 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 1NKP · Crystal structure of Myc-Max recognizing DNA · the same entry in another collection · chain E against E, TM-score 1.00
- P61244 · AlphaFold monomer V2.0 prediction for protein max (P61244) · a predicted model of the same protein · chain B against A, TM-score 0.96
- P01106 · AlphaFold monomer V2.0 prediction for myc proto-oncogene protein (P01106) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 P01106
- Every structure of UniProt P61244
- Elsewhere: RCSB PDB 1NKP · PDBe 1NKP · UniProt P01106 · UniProt P61244
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