Research workbench
Crystal structure of an RNase a dimer displaying a new type of 3D domain swapping
Analyse Crystal structure of an RNase a dimer displaying a new type of 3D domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1F0V
- Type
- protein + DNA
- Length
- 504 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*G)-3'; Ribonuclease a
- EC
- 3.1.27.5
- UniProt
- P61823
- Ligands
- PO4
- Pockets
- 1 · best druggability 0.30
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M, N, O, P | 5'-D(*CP*G)-3' | dna | 2 | — | — |
| A, B, C, D | Ribonuclease a (EC 3.1.27.5) | protein | 124 | 21% helix, 39% strand | P61823 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains P, C, D, M, A, B, N, O
- GOL · Glycerol · additive · 24 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.30 | 0.74 | 16 | empty |
Interfaces
11 interfaces between chains.
- C–D · 1881 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 1844 Ų buried · 37 hydrogen bonds · protein-protein
- N–B · 311 Ų buried · 6 hydrogen bonds · protein-nucleic
- P–D · 298 Ų buried · 5 hydrogen bonds · protein-nucleic
- O–C · 297 Ų buried · 5 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 1F0V · Crystal structure of an Rnase A dimer displaying a new type of 3D domain swapping · 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
- Every structure of UniProt P61823
- Elsewhere: RCSB PDB 1F0V · PDBe 1F0V · UniProt P61823
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