MolNFT v1 · #66140 · protein + RNA
Crystal structure of class I ligase ribozyme self-ligation product, in complex with U1A rbd
3HHN · U1 small nuclear ribonucleoprotein a: “Crystal structure of class I ligase ribozyme self-ligation product, in complex with U1A rbd”. X-ray diffraction, 1 ligand (MG), 11 pockets (best druggability 0.69). MolNFT v1 #66140 on…
- PDB
- 3HHN
- Type
- protein + RNA
- Length
- 459 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- U1 small nuclear ribonucleoprotein a; Class I ligase ribozyme, self-ligation product
- UniProt
- P09012
- Ligands
- MG
- Pockets
- 11 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | U1 small nuclear ribonucleoprotein a | protein | 92 | 33% helix, 23% strand | P09012 |
| C, E | Class I ligase ribozyme, self-ligation product | rna | 137 | — | — |
| D | U1 small nuclear ribonucleoprotein a | protein | 93 | 32% helix, 23% strand | P09012 |
Ligands and binding sites
- MG · Magnesium ion · metal · 34 copies · chains B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 578 | 0.69 | 0.79 | 28 | MG |
| 2 | 433 | 0.69 | 0.81 | 28 | empty |
| 3 | 727 | 0.69 | 0.77 | 38 | MG |
| 4 | 660 | 0.66 | 0.76 | 40 | MG |
| 5 | 412 | 0.65 | 0.79 | 35 | MG |
Interfaces
3 interfaces between chains.
- B–C · 936 Ų buried · 36 hydrogen bonds · protein-nucleic
- D–E · 932 Ų buried · 29 hydrogen bonds · protein-nucleic
- B–D · 195 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3HHN · Crystal structure of class I ligase ribozyme self-ligation product, in complex with U1A… · the same entry in another collection · chain B against B, 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 P09012
- Elsewhere: RCSB PDB 3HHN · PDBe 3HHN · UniProt P09012
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