Research workbench
Crystal structure of RNase T in complex with a di-nucleotide product (gg) with one mg in the active site
Analyse Crystal structure of RNase T in complex with a di-nucleotide product (gg) with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VA0
- Type
- protein + DNA
- Length
- 419 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease T; DNA (5'-D(*GP*G)-3')
- EC
- 3.1.13.-
- UniProt
- P30014
- Ligands
- MG, CO
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease T (EC 3.1.13.-) | protein | 207 | 42% helix, 24% strand | P30014 |
| B | Ribonuclease T (EC 3.1.13.-) | protein | 208 | 40% helix, 24% strand | P30014 |
| C, D | DNA (5'-D(*GP*G)-3') | dna | 2 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.61 | 0.77 | 38 | empty |
| 2 | 189 | 0.56 | 0.80 | 29 | MG |
| 3 | 186 | 0.55 | 0.80 | 29 | MG |
Interfaces
5 interfaces between chains.
- A–B · 1408 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 403 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–D · 401 Ų buried · 4 hydrogen bonds · protein-nucleic
- A–D · 84 Ų buried · 0 hydrogen bonds · protein-nucleic
- B–C · 82 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 3VA0 · Crystal structure of RNase T in complex with a di-nucleotide product (GG) with one Mg in… · the same entry in another collection · chain A against A, TM-score 1.00
- P30014 · AlphaFold monomer V2.0 prediction for ribonuclease T (P30014) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P30014
- Elsewhere: RCSB PDB 3VA0 · PDBe 3VA0 · UniProt P30014
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