Research workbench
Interdomain rrm packing contributes to RNA recognition in the RNA15, HRP1, anchor RNA 3' processing ternary complex
Analyse Interdomain rrm packing contributes to RNA recognition in the RNA15, HRP1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2KM8
- Type
- protein + RNA
- Length
- 264 residues
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(P*UP*AP*UP*AP*UP*AP*UP*AP*AP*UP*AP*AP*U)-3'; MRNA 3'-end-processing protein RNA15…
- UniProt
- P25299, Q99383
- Pockets
- 2 · best druggability 0.74
Structure
solution nmr · 3 distinct chains · 22% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-R(P*UP*AP*UP*AP*UP*AP*UP*AP*AP*UP*AP*AP*U)-3' | rna | 13 | — | — |
| B | MRNA 3'-end-processing protein RNA15 | protein | 84 | 20% helix, 24% strand | P25299 |
| C | Nuclear polyadenylated RNA-binding protein 4 | protein | 167 | 23% helix, 22% strand | Q99383 |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 888 | 0.74 | 0.78 | 76 | empty |
| 2 | 162 | 0.42 | 0.74 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1216 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–B · 635 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–C · 113 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2KM8 · Interdomain RRM packing contributes to RNA recognition in the rna15, hrp1, anchor RNA 3'… · the same entry in another collection · chain A against A, TM-score 1.00
- Q99383 · AlphaFold monomer V2.0 prediction for nuclear polyadenylated RNA- binding protein 4… · a predicted model of the same protein · chain C against A, TM-score 0.76
- P25299 · AlphaFold monomer V2.0 prediction for mRNA 3'-end-processing protein RNA15 (P25299) · a predicted model of the same protein · chain B against A, TM-score 0.68
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 P25299
- Every structure of UniProt Q99383
- Elsewhere: RCSB PDB 2KM8 · PDBe 2KM8 · UniProt P25299 · UniProt Q99383
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