Research workbench
Crystal structure of yeast RNase III (RNT1P) complexed with a non- hydrolyzable RNA substrate analog
Analyse Crystal structure of yeast RNase III (RNT1P) complexed with a non- hydrolyzable… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T16
- Type
- protein + RNA
- Length
- 2,142 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease 3; RNA substrate analog
- EC
- 3.1.26.3
- UniProt
- Q02555
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 10 distinct chains · 62% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, I | Ribonuclease 3 (EC 3.1.26.3) | protein | 276 | 52% helix, 8% strand | Q02555 |
| B | Ribonuclease 3 (EC 3.1.26.3) | protein | 269 | 55% helix, 8% strand | Q02555 |
| C | Ribonuclease 3 (EC 3.1.26.3) | protein | 113 | 72% helix, 0% strand | Q02555 |
| D, L | Ribonuclease 3 (EC 3.1.26.3) | protein | 116 | 72% helix, 0% strand | Q02555 |
| E, F | Ribonuclease 3 (EC 3.1.26.3) | protein | 115 | 70% helix, 0% strand | Q02555 |
| G, H, O, P | RNA substrate analog | rna | 34 | — | — |
| J | Ribonuclease 3 (EC 3.1.26.3) | protein | 267 | 56% helix, 8% strand | Q02555 |
| K | Ribonuclease 3 (EC 3.1.26.3) | protein | 114 | 70% helix, 0% strand | Q02555 |
| M | Ribonuclease 3 (EC 3.1.26.3) | protein | 112 | 71% helix, 0% strand | Q02555 |
| N | Ribonuclease 3 (EC 3.1.26.3) | protein | 117 | 69% helix, 0% strand | Q02555 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, F, E, H, I, J, N, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 906 | 0.82 | 0.85 | 80 | empty |
| 2 | 898 | 0.82 | 0.84 | 60 | empty |
| 3 | 790 | 0.81 | 0.84 | 77 | empty |
| 4 | 694 | 0.79 | 0.84 | 50 | empty |
| 5 | 1144 | 0.76 | 0.79 | 101 | EDO |
Interfaces
46 interfaces between chains.
- M–N · 3660 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 3611 Ų buried · 23 hydrogen bonds · protein-protein
- K–L · 3599 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 3469 Ų buried · 24 hydrogen bonds · protein-protein
- I–J · 1467 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 5T16 · Crystal structure of yeast RNase III (Rnt1p) complexed with a non-hydrolyzable RNA… · the same entry in another collection · chain I against I, 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 Q02555
- Elsewhere: RCSB PDB 5T16 · PDBe 5T16 · UniProt Q02555
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