Research workbench
Crystal structure of ctsr in complex with a 26BP DNA duplex
Analyse Crystal structure of ctsr in complex with a 26BP DNA duplex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H0D
- Type
- protein + DNA
- Length
- 358 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ctsr; DNA (26-mer)
- Ligands
- PO4
- Pockets
- 1 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 56% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ctsr | protein | 155 | 55% helix, 14% strand | — |
| B | Ctsr | protein | 151 | 57% helix, 11% strand | — |
| C | DNA (26-mer) | dna | 26 | — | — |
| D | DNA (26-mer) | dna | 26 | — | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 822 | 0.67 | 0.74 | 60 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1134 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1102 Ų buried · 88 hydrogen bonds · nucleic-nucleic
- B–D · 590 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–D · 576 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–C · 498 Ų buried · 17 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3H0D · Crystal structure of CtsR in complex with a 26bp DNA duplex · 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
- Elsewhere: RCSB PDB 3H0D · PDBe 3H0D
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