Research workbench
Aspa-32MER DNA,CRYSTAL form 2
Analyse Aspa-32MER DNA,CRYSTAL form 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K5R
- 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
- 12 · best druggability 0.65
Structure
x-ray diffraction · 6 distinct chains · 56% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | Aspa | protein | 91 | 54% helix, 15% strand | O93706 |
| D | Aspa | protein | 90 | 58% helix, 13% strand | O93706 |
| A | Aspa | protein | 89 | 55% helix, 13% strand | O93706 |
| B, F | Aspa | protein | 92 | 58% helix, 17% strand | O93706 |
| P | DNA (32-mer) | dna | 32 | — | — |
| N | DNA (32-mer) | dna | 32 | — | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 9 copies · chains D, A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 302 | 0.65 | 0.81 | 33 | empty |
| 2 | 385 | 0.61 | 0.78 | 39 | empty |
| 3 | 295 | 0.61 | 0.79 | 30 | empty |
| 4 | 58 | 0.54 | 0.88 | 16 | empty |
| 5 | 115 | 0.53 | 0.82 | 23 | PO4 |
Interfaces
21 interfaces between chains.
- E–F · 1573 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1557 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1509 Ų buried · 8 hydrogen bonds · protein-protein
- P–N · 1379 Ų buried · 123 hydrogen bonds · nucleic-nucleic
- B–P · 564 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 5K5R · AspA-32mer DNA,crystal form 2 · the same entry in another collection · chain E against E, 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 5K5R · PDBe 5K5R · UniProt O93706
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