Research workbench
Crystal structure of RNase T (E92G mutant)
Analyse Crystal structure of RNase T (E92G mutant) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NGY
- Type
- protein
- Length
- 796 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease T; His tag sequence
- EC
- 3.1.13.-
- UniProt
- P30014
- Ligands
- CO
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease T (EC 3.1.13.-) | protein | 204 | 40% helix, 25% strand | P30014 |
| B, D | Ribonuclease T (EC 3.1.13.-) | protein | 202 | 41% helix, 24% strand | P30014 |
| C | Ribonuclease T (EC 3.1.13.-) | protein | 182 | 41% helix, 27% strand | P30014 |
| E | His tag sequence | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1056 | 0.85 | 0.86 | 118 | empty |
| 2 | 104 | 0.70 | 0.93 | 23 | empty |
| 3 | 268 | 0.60 | 0.79 | 34 | empty |
| 4 | 165 | 0.59 | 0.82 | 22 | empty |
| 5 | 144 | 0.51 | 0.80 | 25 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1441 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1363 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 624 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 546 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 355 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
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 3NGY · PDBe 3NGY · UniProt P30014
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