MolNFT v1 · #75396 · protein + DNA
Crystal structure of a sox-DNA complex
3POV · Orf 37: “Crystal structure of a sox-DNA complex”. X-ray diffraction, 1 ligand (MG), 8 pockets (best druggability 0.74). MolNFT v1 #75396 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3POV
- Type
- protein + DNA
- Length
- 483 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orf 37; DNA (5'- D(*GP*GP*GP*AP*TP*CP*CP*TP*CP*CP*CP*AP*GP*TP*CP*GP*AP*CP*C)-3'); DNA…
- UniProt
- P88925
- Ligands
- MG
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orf 37 | protein | 445 | 40% helix, 15% strand | P88925 |
| C | DNA (5'- D(*GP*GP*GP*AP*TP*CP*CP*TP*CP*CP*CP*AP*GP*TP*CP*GP*AP*CP*C)-3') | dna | 19 | — | — |
| D | DNA (5'- D(*GP*GP*TP*CP*GP*AP*CP*TP*AP*GP*GP*AP*GP*GP*AP*TP*CP*CP*C)-3') | dna | 19 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 754 | 0.74 | 0.80 | 48 | empty |
| 2 | 457 | 0.66 | 0.78 | 45 | MG, FMT |
| 3 | 98 | 0.45 | 0.79 | 18 | empty |
| 4 | 134 | 0.45 | 0.77 | 25 | empty |
| 5 | 158 | 0.44 | 0.75 | 31 | empty |
Interfaces
3 interfaces between chains.
- C–D · 830 Ų buried · 96 hydrogen bonds · nucleic-nucleic
- A–C · 407 Ų buried · 4 hydrogen bonds · protein-nucleic
- A–D · 295 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 3POV · Crystal structure of a SOX-DNA complex · the same entry in another collection · chain A against A, 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 P88925
- Elsewhere: RCSB PDB 3POV · PDBe 3POV · UniProt P88925
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