Research workbench
Structure of stenofolia protein hd domain bound with DNA
Analyse Structure of stenofolia protein hd domain bound with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WIG
- Type
- protein + DNA
- Length
- 196 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Stenofolia; DNA (5'- D(P*GP*CP*AP*AP*AP*TP*TP*AP*AP*TP*GP*AP*TP*TP*TP*AP*TP*TP*CP*AP*AP*G)…
- UniProt
- G0ZGT3
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 64% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Stenofolia | protein | 84 | 63% helix, 0% strand | G0ZGT3 |
| B | Stenofolia | protein | 68 | 66% helix, 0% strand | G0ZGT3 |
| C | DNA (5'- D(P*GP*CP*AP*AP*AP*TP*TP*AP*AP*TP*GP*AP*TP*TP*TP*AP*TP*TP*CP*AP*AP*G) -3') | dna | 22 | — | — |
| D | DNA (5'- D(P*CP*TP*TP*GP*AP*AP*TP*AP*AP*AP*TP*CP*AP*TP*TP*AP*AP*TP*TP*TP*GP*C) -3') | dna | 22 | — | — |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.60 | 0.78 | 43 | empty |
| 2 | 97 | 0.44 | 0.80 | 20 | empty |
| 3 | 109 | 0.43 | 0.78 | 18 | empty |
Interfaces
5 interfaces between chains.
- C–D · 945 Ų buried · 72 hydrogen bonds · nucleic-nucleic
- A–D · 523 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–C · 454 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–C · 450 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–D · 433 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 6WIG · Structure of STENOFOLIA Protein HD domain bound with DNA · 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 G0ZGT3
- Elsewhere: RCSB PDB 6WIG · PDBe 6WIG · UniProt G0ZGT3
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