Research workbench
X-ray structure of the complex of bovine seminal ribonuclease swapping dimer with D(CPA)
Analyse X-ray structure of the complex of bovine seminal ribonuclease swapping dimer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1R5C
- Type
- protein
- Length
- 248 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease, seminal
- EC
- 3.1.27.5
- UniProt
- P00669
- Ligands
- CPA
- Pockets
- 2 · best druggability 0.43
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribonuclease, seminal (EC 3.1.27.5) | protein | 124 | 23% helix, 35% strand | P00669 |
Ligands and binding sites
- CPA · 2'-deoxycytidine-2'-deoxyadenosine-3',5'-monophosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 175 | 0.43 | 0.74 | 22 | empty |
| 2 | 156 | 0.40 | 0.73 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1960 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 1R5C · X-ray structure of the complex of Bovine seminal ribonuclease swapping dimer with d(CpA) · the same entry in another collection · chain A against A, TM-score 1.00
- P00669 · AlphaFold monomer V2.0 prediction for seminal ribonuclease (P00669) · a predicted model of the same protein · chain A against A, TM-score 0.82
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 P00669
- Elsewhere: RCSB PDB 1R5C · PDBe 1R5C · UniProt P00669
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