MolNFT v1 · #29711 · protein + RNA
Structural basis for recognition of uuuoh 3'-terminii of nascent RNA pol III transcripts by la autoantigen
1ZH5 · 5'-R(*UP*GP*CP*UP*GP*UP*UP*UP*U)-3': “Structural basis for recognition of uuuoh 3'-terminii of nascent RNA pol III transcripts by la autoantigen”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.67). MolNFT v1…
- PDB
- 1ZH5
- Type
- protein + RNA
- Length
- 387 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*UP*GP*CP*UP*GP*UP*UP*UP*U)-3'; Lupus la protein
- UniProt
- P05455
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | 5'-R(*UP*GP*CP*UP*GP*UP*UP*UP*U)-3' | rna | 9 | — | — |
| A | Lupus la protein | protein | 185 | 41% helix, 21% strand | P05455 |
| B | Lupus la protein | protein | 184 | 40% helix, 21% strand | P05455 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.67 | 0.78 | 50 | empty |
| 2 | 406 | 0.60 | 0.76 | 31 | SO4 |
| 3 | 360 | 0.57 | 0.75 | 35 | SO4 |
| 4 | 382 | 0.55 | 0.74 | 37 | empty |
| 5 | 63 | 0.42 | 0.82 | 16 | empty |
Interfaces
6 interfaces between chains.
- C–B · 560 Ų buried · 8 hydrogen bonds · protein-nucleic
- D–A · 544 Ų buried · 8 hydrogen bonds · protein-nucleic
- D–B · 399 Ų buried · 9 hydrogen bonds · protein-nucleic
- C–A · 372 Ų buried · 3 hydrogen bonds · protein-nucleic
- C–D · 225 Ų buried · 15 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 1ZH5 · Structural basis for recognition of UUUOH 3'-terminii of nascent RNA pol III transcripts… · the same entry in another collection · chain C against C, TM-score 1.00
- P05455 · AlphaFold monomer V2.0 prediction for lupus la protein (P05455) · a predicted model of the same protein · chain B 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 P05455
- Elsewhere: RCSB PDB 1ZH5 · PDBe 1ZH5 · UniProt P05455
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