Research workbench
Structure of PNOB8 aspa-DNA complex.
Analyse Structure of PNOB8 aspa-DNA complex. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KK1
- Type
- protein + DNA
- Length
- 607 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspa; DNA (31-mer)
- UniProt
- O93706
- Pockets
- 11 · best druggability 0.64
Structure
x-ray diffraction · 5 distinct chains · 56% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D, E | Aspa | protein | 91 | 54% helix, 16% strand | O93706 |
| A | Aspa | protein | 88 | 57% helix, 13% strand | O93706 |
| B, F | Aspa | protein | 92 | 59% helix, 16% strand | O93706 |
| P | DNA (31-mer) | dna | 31 | — | — |
| N | DNA (31-mer) | dna | 31 | — | — |
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 249 | 0.64 | 0.83 | 35 | empty |
| 2 | 499 | 0.63 | 0.76 | 46 | empty |
| 3 | 356 | 0.60 | 0.77 | 35 | empty |
| 4 | 149 | 0.49 | 0.79 | 21 | empty |
| 5 | 55 | 0.47 | 0.85 | 16 | empty |
Interfaces
21 interfaces between chains.
- E–F · 1623 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1581 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1475 Ų buried · 10 hydrogen bonds · protein-protein
- P–N · 1328 Ų buried · 116 hydrogen bonds · nucleic-nucleic
- B–N · 578 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 5KK1 · Structure of pNOB8 AspA-DNA complex. · the same entry in another collection · chain C against C, 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 O93706
- Elsewhere: RCSB PDB 5KK1 · PDBe 5KK1 · UniProt O93706
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