Research workbench
Structure of aspa-DNA complex: novel centromere bindng protein- centromere complex
Analyse Structure of aspa-DNA complex: novel centromere bindng protein- centromere… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K5Q
- Type
- protein + DNA
- Length
- 609 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspa; DNA (32-mer)
- UniProt
- O93706
- Ligands
- PO4
- Pockets
- 10 · best druggability 0.67
Structure
x-ray diffraction · 6 distinct chains · 58% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | Aspa | protein | 91 | 57% helix, 14% strand | O93706 |
| D | Aspa | protein | 90 | 57% helix, 17% strand | O93706 |
| A | Aspa | protein | 89 | 58% helix, 17% strand | O93706 |
| B, F | Aspa | protein | 92 | 59% helix, 13% strand | O93706 |
| P | DNA (32-mer) | dna | 32 | — | — |
| N | DNA (32-mer) | dna | 32 | — | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.67 | 0.83 | 35 | empty |
| 2 | 289 | 0.64 | 0.81 | 36 | empty |
| 3 | 369 | 0.63 | 0.79 | 31 | empty |
| 4 | 375 | 0.62 | 0.78 | 32 | empty |
| 5 | 82 | 0.35 | 0.75 | 20 | PO4 |
Interfaces
21 interfaces between chains.
- E–F · 1600 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1559 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1524 Ų buried · 8 hydrogen bonds · protein-protein
- P–N · 1412 Ų buried · 138 hydrogen bonds · nucleic-nucleic
- B–N · 569 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 5K5Q · Structure of AspA-DNA complex: novel centromere bindng protein-centromere 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 5K5Q · PDBe 5K5Q · UniProt O93706
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