MolNFT v1 · #139438 · protein + DNA
Ternary complex of MTF2, DNA and histone
5XFR · Metal-response element-binding transcription factor 2: “Ternary complex of MTF2, DNA and histone”. X-ray diffraction, 1 ligand (ZN), 10 pockets (best druggability 0.63). MolNFT v1 #139438 on GenesisL1: 3D structure, binding sites…
- PDB
- 5XFR
- Type
- protein + DNA
- Length
- 639 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metal-response element-binding transcription factor 2; Peptide from histone H3.1; DNA…
- UniProt
- Q9Y483, P68431
- Ligands
- ZN
- Pockets
- 10 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metal-response element-binding transcription factor 2 | protein | 309 | 27% helix, 21% strand | Q9Y483 |
| B | Metal-response element-binding transcription factor 2 | protein | 298 | 27% helix, 20% strand | Q9Y483 |
| C, D | Peptide from histone H3.1 | protein | 3 | 0% helix, 0% strand | P68431 |
| E, F | DNA (5'-D(*GP*GP*GP*CP*GP*GP*CP*CP*GP*CP*CP*CP*T)-3') | dna | 13 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 640 | 0.63 | 0.74 | 48 | empty |
| 2 | 448 | 0.63 | 0.77 | 49 | empty |
| 3 | 272 | 0.55 | 0.76 | 33 | empty |
| 4 | 110 | 0.46 | 0.79 | 16 | empty |
| 5 | 64 | 0.45 | 0.83 | 16 | empty |
Interfaces
6 interfaces between chains.
- E–F · 571 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- A–B · 406 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 319 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 317 Ų buried · 1 hydrogen bond · protein-protein
- B–E · 309 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (methylation).
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 Q9Y483
- Every structure of UniProt P68431
- Elsewhere: RCSB PDB 5XFR · PDBe 5XFR · UniProt Q9Y483 · UniProt P68431
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