Research workbench
Crystal structure of human RPRD1B, carboxy-terminal domain
Analyse Crystal structure of human RPRD1B, carboxy-terminal domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FLA
- Type
- protein
- Length
- 504 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Regulation of nuclear pre-mRNA domain-containing protein 1B
- UniProt
- Q9NQG5
- Ligands
- UNX
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 90% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Regulation of nuclear pre-mRNA domain-containing protein 1B | protein | 126 | 90% helix, 0% strand | Q9NQG5 |
| B | Regulation of nuclear pre-mRNA domain-containing protein 1B | protein | 124 | 90% helix, 0% strand | Q9NQG5 |
| C, D | Regulation of nuclear pre-mRNA domain-containing protein 1B | protein | 127 | 91% helix, 0% strand | Q9NQG5 |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 7 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 587 | 0.62 | 0.74 | 58 | empty |
| 2 | 204 | 0.53 | 0.77 | 25 | empty |
| 3 | 53 | 0.27 | 0.74 | 12 | empty |
Interfaces
5 interfaces between chains.
- C–D · 3183 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 3126 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 343 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 304 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 41 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4FLA · Crystal structure of human RPRD1B, carboxy-terminal domain · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NQG5 · AlphaFold monomer V2.0 prediction for regulation of nuclear pre-mRNA domain-containing… · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q9NQG5
- Elsewhere: RCSB PDB 4FLA · PDBe 4FLA · UniProt Q9NQG5
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