Research workbench
Crystal structure of RNase T in complex with a preferred ssdna (aat) with two mg in the active site
Analyse Crystal structure of RNase T in complex with a preferred ssdna (aat) with two… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V9U
- Type
- protein + DNA
- Length
- 841 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease T; DNA (5'-D(*TP*TP*AP*CP*AP*AP*T)-3')
- EC
- 3.1.13.-
- UniProt
- P30014
- Ligands
- MG, CO
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 6 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease T (EC 3.1.13.-) | protein | 206 | 43% helix, 24% strand | P30014 |
| B | Ribonuclease T (EC 3.1.13.-) | protein | 207 | 41% helix, 24% strand | P30014 |
| C | Ribonuclease T (EC 3.1.13.-) | protein | 207 | 41% helix, 24% strand | P30014 |
| D | Ribonuclease T (EC 3.1.13.-) | protein | 210 | 39% helix, 23% strand | P30014 |
| E | DNA (5'-D(*TP*TP*AP*CP*AP*AP*T)-3') | dna | 2 | — | — |
| F, G, H | DNA (5'-D(*TP*TP*AP*CP*AP*AP*T)-3') | dna | 3 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, E, B, F, C, G, D, H
- CO · Cobalt (II) ion · metal · 5 copies · chains A, B, C, G, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 501 | 0.68 | 0.79 | 61 | empty |
| 2 | 484 | 0.63 | 0.76 | 38 | empty |
| 3 | 452 | 0.62 | 0.76 | 33 | empty |
| 4 | 55 | 0.30 | 0.75 | 15 | empty |
Interfaces
11 interfaces between chains.
- C–D · 1473 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1378 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 632 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 504 Ų buried · 7 hydrogen bonds · protein-nucleic
- C–G · 479 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3V9U · Crystal structure of RNase T in complex with a preferred ssDNA (AAT) with two Mg in the… · the same entry in another collection · chain H against H, TM-score 1.00
- P30014 · AlphaFold monomer V2.0 prediction for ribonuclease T (P30014) · a predicted model of the same protein · chain C 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 3V9U · PDBe 3V9U · UniProt P30014
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