Research workbench
Ribonuclease T1 (THR93GLN mutant) complexed with 2'GMP
Analyse Ribonuclease T1 (THR93GLN mutant) complexed with 2'GMP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HOH
- Type
- protein
- Length
- 416 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (ribonuclease T1)
- EC
- 3.1.27.3
- UniProt
- P00651
- Ligands
- 2GP, CA
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Protein (ribonuclease T1) (EC 3.1.27.3) | protein | 104 | 16% helix, 29% strand | P00651 |
Ligands and binding sites
- 2GP · Guanosine-2'-monophosphate · ligand · 5 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.45 | 0.73 | 24 | empty |
| 2 | 117 | 0.40 | 0.76 | 28 | empty |
| 3 | 74 | 0.37 | 0.78 | 23 | 2GP |
Interfaces
3 interfaces between chains.
- A–C · 463 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 139 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 16 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3HOH · Ribonuclease T1 (THR93GLN mutant) complexed with 2'GMP · 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 P00651
- Elsewhere: RCSB PDB 3HOH · PDBe 3HOH · UniProt P00651
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