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Structure of omomyc bound to double-stranded DNA
Analyse Structure of omomyc bound to double-stranded DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I50
- Type
- protein + DNA
- Length
- 232 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myc proto-oncogene protein; DNA (5'- D(P*CP*AP*CP*CP*CP*GP*GP*TP*CP*AP*CP*GP*TP*GP*GP*CP*C…
- UniProt
- P01106
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myc proto-oncogene protein | protein | 92 | 82% helix, 0% strand | P01106 |
| B | Myc proto-oncogene protein | protein | 96 | 76% helix, 0% strand | P01106 |
| C | DNA (5'- D(P*CP*AP*CP*CP*CP*GP*GP*TP*CP*AP*CP*GP*TP*GP*GP*CP*CP*TP*AP*CP*AP*C) -3') | dna | 22 | — | — |
| D | DNA (5'- D(P*GP*TP*GP*TP*AP*GP*GP*CP*CP*AP*CP*GP*TP*GP*AP*CP*CP*GP*GP*GP*TP*G) -3') | dna | 22 | — | — |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.81 | 0.93 | 26 | empty |
| 2 | 228 | 0.50 | 0.76 | 20 | empty |
| 3 | 173 | 0.44 | 0.74 | 16 | empty |
| 4 | 121 | 0.42 | 0.76 | 19 | empty |
| 5 | 51 | 0.23 | 0.72 | 13 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1677 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 1000 Ų buried · 111 hydrogen bonds · nucleic-nucleic
- A–D · 535 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–C · 510 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–D · 253 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
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 P01106
- Elsewhere: RCSB PDB 5I50 · PDBe 5I50 · UniProt P01106
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