MolNFT v1 · #30305 · protein + RNA
Crystal structure of a group I INTRON/TWO exon complex that includes all catalytic metal ion ligands.
1ZZN · 197-mer: “Crystal structure of a group I INTRON/TWO exon complex that includes all catalytic metal ion ligands.”. X-ray diffraction, 2 ligands (MG, K), 8 pockets (best druggability 0.77). MolNFT v1 #30305 on GenesisL1: 3D structure…
- PDB
- 1ZZN
- Type
- protein + RNA
- Length
- 317 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 197-mer; 5'-R(*AP*AP*GP*CP*CP*AP*CP*AP*CP*AP*AP*AP*CP*CP*AP*GP*AP*CP *GP*GP*CP*C)-3'…
- UniProt
- P09012
- Ligands
- MG, K
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 197-mer | rna | 197 | — | — |
| C | 5'-R(*AP*AP*GP*CP*CP*AP*CP*AP*CP*AP*AP*AP*CP*CP*AP*GP*AP*CP *GP*GP*CP*C)-3' | rna | 22 | — | — |
| D | 5'-R(*CP*AP*(5MU))-3' | rna | 3 | — | — |
| A | U1 small nuclear ribonucleoprotein a RNA binding domain | protein | 95 | 24% helix, 18% strand | P09012 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 562 | 0.77 | 0.85 | 45 | empty |
| 2 | 769 | 0.74 | 0.80 | 36 | empty |
| 3 | 1028 | 0.68 | 0.74 | 54 | MG |
| 4 | 384 | 0.58 | 0.77 | 29 | empty |
| 5 | 475 | 0.58 | 0.75 | 30 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1945 Ų buried · 124 hydrogen bonds · nucleic-nucleic
- B–A · 932 Ų buried · 27 hydrogen bonds · protein-nucleic
- B–D · 407 Ų buried · 23 hydrogen bonds · nucleic-nucleic
- C–D · 104 Ų buried · 6 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 3 modified (nucleotide modification).
Compared structures
- 1ZZN · Crystal structure of a group I intron/two exon complex that includes all catalytic metal… · 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 1ZZN · PDBe 1ZZN · UniProt P09012
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