MolNFT v1 · #189305 · protein + DNA
Selenomethionine mutant (L740SEM) of BEN4 domain of protein BEND3 with DNA
7V9F · Ben domain-containing protein 3: “Selenomethionine mutant (L740SEM) of BEN4 domain of protein BEND3 with DNA”. X-ray diffraction, 2 pockets (best druggability 0.55). MolNFT v1 #189305 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7V9F
- Type
- protein + DNA
- Length
- 139 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ben domain-containing protein 3; DNA (5'-D(*TP*GP*GP*CP*CP*CP*CP*AP*CP*GP*CP*GP*GP*TP*GP*C…
- UniProt
- Q6PAL0
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 65% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ben domain-containing protein 3 | protein | 107 | 65% helix, 4% strand | Q6PAL0 |
| B | DNA (5'-D(*TP*GP*GP*CP*CP*CP*CP*AP*CP*GP*CP*GP*GP*TP*GP*C)- 3') | dna | 16 | — | — |
| C | DNA (5'-D(*GP*CP*AP*CP*CP*GP*CP*GP*TP*GP*GP*GP*GP*CP*CP*A)- 3') | dna | 16 | — | — |
Ligands and binding sites
- CIT · Citric acid · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 372 | 0.55 | 0.73 | 27 | empty |
| 2 | 66 | 0.26 | 0.72 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–C · 732 Ų buried · 74 hydrogen bonds · nucleic-nucleic
- A–C · 171 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–B · 125 Ų buried · 4 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (engineered).
Compared structures
- 7V9F · Selenomethionine mutant (L740Sem) of BEN4 domain of protein Bend3 with DNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q6PAL0 · AlphaFold monomer V2.0 prediction for ben domain-containing protein 3 (Q6PAL0) · a predicted model of the same protein · chain A against A, TM-score 0.63
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 Q6PAL0
- Elsewhere: RCSB PDB 7V9F · PDBe 7V9F · UniProt Q6PAL0
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