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Three-dimensional structure of ribonulcease T1 complexed with an isosteric phosphonate analogue of gpu: alternate substrate binding modes and catalysis.
Analyse Three-dimensional structure of ribonulcease T1 complexed with an isosteric… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1B2M
- Type
- protein + RNA
- Length
- 214 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*GP*(U34))-3'; Ribonuclease T1
- EC
- 3.1.27.3
- UniProt
- P00651
- Pockets
- 2 · best druggability 0.35
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D, E | 5'-R(*GP*(U34))-3' | rna | 2 | — | — |
| A, B | Ribonuclease T1 (EC 3.1.27.3) | protein | 104 | 15% helix, 31% strand | P00651 |
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 | 71 | 0.35 | 0.77 | 13 | empty |
| 2 | 58 | 0.34 | 0.78 | 16 | empty |
Interfaces
8 interfaces between chains.
- C–A · 314 Ų buried · 12 hydrogen bonds · protein-nucleic
- D–B · 305 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–B · 278 Ų buried · 7 hydrogen bonds · protein-protein
- D–A · 199 Ų buried · 0 hydrogen bonds · protein-nucleic
- E–B · 101 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 4 disulfide, 3 modified (disulfide, nucleotide modification).
Compared structures
- 1B2M · Three-dimensional structure of ribonulcease T1 complexed with an isosteric phosphonate… · the same entry in another collection · chain A against A, TM-score 1.00
- P00651 · AlphaFold monomer V2.0 prediction for guanyl-specific ribonuclease T1 (P00651) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P00651
- Elsewhere: RCSB PDB 1B2M · PDBe 1B2M · UniProt P00651
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