Research workbench
Shuguo pwwp in complex with ssdna
Analyse Shuguo pwwp in complex with ssdna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KCP
- Type
- protein + DNA
- Length
- 335 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LD23804P; DNA (5'-D(P*TP*TP*TP*TP*T)-3')
- UniProt
- Q9VAA9
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LD23804P | protein | 83 | 40% helix, 34% strand | Q9VAA9 |
| B | LD23804P | protein | 84 | 40% helix, 33% strand | Q9VAA9 |
| C | LD23804P | protein | 81 | 41% helix, 33% strand | Q9VAA9 |
| E | DNA (5'-D(P*TP*TP*TP*TP*T)-3') | dna | 2 | — | — |
| D | LD23804P | protein | 85 | 40% helix, 32% strand | Q9VAA9 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.69 | 0.92 | 18 | empty |
| 2 | 566 | 0.65 | 0.76 | 46 | empty |
| 3 | 109 | 0.41 | 0.76 | 23 | empty |
| 4 | 58 | 0.36 | 0.78 | 18 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1563 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1551 Ų buried · 16 hydrogen bonds · protein-protein
- B–E · 333 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–D · 273 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 60 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 6KCP · Shuguo PWWP in complex with ssDNA · 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 Q9VAA9
- Elsewhere: RCSB PDB 6KCP · PDBe 6KCP · UniProt Q9VAA9
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