MolNFT v1 · #176702 · protein + DNA
Structure of sulfolobus solfataricus segb-DNA complex
7DV2: “Structure of sulfolobus solfataricus segb-DNA complex”. X-ray diffraction, 5 pockets (best druggability 0.66). MolNFT v1 #176702 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7DV2
- Type
- protein + DNA
- Length
- 340 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Segb; DNA (5'- D(P*AP*CP*GP*TP*AP*GP*AP*AP*GP*AP*GP*TP*CP*TP*AP*GP*AP*CP*TP*G)-3'); DNA…
- UniProt
- Q981B2
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 5 distinct chains · 64% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Segb | protein | 76 | 64% helix, 7% strand | Q981B2 |
| B, D | Segb | protein | 74 | 64% helix, 7% strand | Q981B2 |
| C | Segb | protein | 75 | 65% helix, 7% strand | Q981B2 |
| E | DNA (5'- D(P*AP*CP*GP*TP*AP*GP*AP*AP*GP*AP*GP*TP*CP*TP*AP*GP*AP*CP*TP*G)-3') | dna | 20 | — | — |
| F | DNA (5'- D(P*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*TP*CP*TP*TP*CP*TP*AP*CP*GP*TP*A)- 3') | dna | 21 | — | — |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.66 | 0.78 | 49 | empty |
| 2 | 142 | 0.57 | 0.83 | 24 | empty |
| 3 | 105 | 0.36 | 0.74 | 16 | empty |
| 4 | 74 | 0.33 | 0.75 | 15 | empty |
| 5 | 81 | 0.30 | 0.73 | 13 | empty |
Interfaces
12 interfaces between chains.
- C–D · 2586 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 2537 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 872 Ų buried · 69 hydrogen bonds · nucleic-nucleic
- C–F · 298 Ų buried · 2 hydrogen bonds · protein-nucleic
- A–E · 288 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 7DV2 · Structure of Sulfolobus solfataricus SegB-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 Q981B2
- Elsewhere: RCSB PDB 7DV2 · PDBe 7DV2 · UniProt Q981B2
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