MolNFT v1 · #55090 · protein + RNA
Structure a of CRISPR endoribonuclease CSE3 bound to 19 nt RNA
2Y9H: “Structure a of CRISPR endoribonuclease CSE3 bound to 19 nt RNA”. X-ray diffraction, 20 pockets (best druggability 0.81). MolNFT v1 #55090 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2Y9H
- Type
- protein + RNA
- Length
- 1,734 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CSE3; 5'-R(*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP *GP*GP*DGP*AP*UP)-3'
- UniProt
- Q53WG9
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 9 distinct chains · 27% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CSE3 | protein | 213 | 24% helix, 35% strand | Q53WG9 |
| B, D, F, H, J, L, N, P | 5'-R(*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP *GP*GP*DGP*AP*UP)-3' | rna | 18 | — | — |
| C | CSE3 | protein | 211 | 25% helix, 35% strand | Q53WG9 |
| E | CSE3 | protein | 211 | 26% helix, 34% strand | Q53WG9 |
| G | CSE3 | protein | 199 | 27% helix, 37% strand | Q53WG9 |
| I | CSE3 | protein | 195 | 29% helix, 34% strand | Q53WG9 |
| K | CSE3 | protein | 191 | 29% helix, 35% strand | Q53WG9 |
| M | CSE3 | protein | 193 | 28% helix, 35% strand | Q53WG9 |
| O | CSE3 | protein | 177 | 25% helix, 27% strand | Q53WG9 |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1011 | 0.81 | 0.82 | 101 | empty |
| 2 | 948 | 0.80 | 0.82 | 62 | empty |
| 3 | 1116 | 0.80 | 0.82 | 73 | empty |
| 4 | 556 | 0.72 | 0.81 | 49 | empty |
| 5 | 650 | 0.72 | 0.79 | 56 | empty |
Interfaces
28 interfaces between chains.
- A–B · 1109 Ų buried · 31 hydrogen bonds · protein-nucleic
- C–D · 1096 Ų buried · 24 hydrogen bonds · protein-nucleic
- G–H · 1062 Ų buried · 31 hydrogen bonds · protein-nucleic
- E–F · 1057 Ų buried · 30 hydrogen bonds · protein-nucleic
- I–J · 1000 Ų buried · 22 hydrogen bonds · protein-nucleic
Compared structures
- 2Y9H · Structure A of CRISPR endoribonuclease Cse3 bound to 19 nt RNA · the same entry in another collection · chain P against P, 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 Q53WG9
- Elsewhere: RCSB PDB 2Y9H · PDBe 2Y9H · UniProt Q53WG9
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