MolNFT v1 · #120049 · protein + DNA
Structure of a transcription factor and DNA complex
5GNJ · Transcription factor MYC2: “Structure of a transcription factor and DNA complex”. X-ray diffraction, 16 pockets (best druggability 0.82). MolNFT v1 #120049 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5GNJ
- Type
- protein + DNA
- Length
- 699 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription factor MYC2; DNA (5'-D(*AP*GP*GP*AP*AP*CP*AP*CP*GP*TP*GP*AP*CP*CP*C)- 3')…
- UniProt
- Q39204
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 10 distinct chains · 82% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, F, M, N | Transcription factor MYC2 | protein | 73 | 81% helix, 0% strand | Q39204 |
| I | Transcription factor MYC2 | protein | 75 | 81% helix, 0% strand | Q39204 |
| K, C, H | DNA (5'-D(*AP*GP*GP*AP*AP*CP*AP*CP*GP*TP*GP*AP*CP*CP*C)- 3') | dna | 14 | — | — |
| L, D | DNA (5'-D(*TP*GP*GP*GP*TP*CP*AP*CP*GP*TP*GP*TP*TP*CP*C)- 3') | dna | 14 | — | — |
| A | Transcription factor MYC2 | protein | 74 | 85% helix, 0% strand | Q39204 |
| B | Transcription factor MYC2 | protein | 77 | 79% helix, 0% strand | Q39204 |
| E | Transcription factor MYC2 | protein | 73 | 85% helix, 0% strand | Q39204 |
| J | DNA (5'-D(*TP*GP*GP*GP*TP*CP*AP*CP*GP*TP*GP*TP*TP*CP*C)- 3') | dna | 13 | — | — |
| O | DNA (5'-D(*AP*GP*GP*AP*AP*CP*AP*CP*GP*TP*GP*AP*CP*CP*C)- 3') | dna | 13 | — | — |
| P | DNA (5'-D(*TP*GP*GP*GP*TP*CP*AP*CP*GP*TP*GP*TP*TP*CP*C)- 3') | dna | 12 | — | — |
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.82 | 0.94 | 26 | empty |
| 2 | 231 | 0.82 | 0.95 | 22 | empty |
| 3 | 214 | 0.81 | 0.95 | 21 | empty |
| 4 | 769 | 0.78 | 0.82 | 59 | empty |
| 5 | 422 | 0.59 | 0.76 | 30 | empty |
Interfaces
39 interfaces between chains.
- M–N · 1691 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 1685 Ų buried · 2 hydrogen bonds · protein-protein
- G–I · 1636 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 1634 Ų buried · 6 hydrogen bonds · protein-protein
- K–L · 616 Ų buried · 51 hydrogen bonds · nucleic-nucleic
Compared structures
- 5GNJ · Structure of a transcription factor and DNA complex · the same entry in another collection · chain P against P, TM-score 1.00
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 Q39204
- Elsewhere: RCSB PDB 5GNJ · PDBe 5GNJ · UniProt Q39204
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