Research workbench
Human RPRD1B cid in complex with a RPB1-ctd derived SER2 phosphorylated peptide
Analyse Human RPRD1B cid in complex with a RPB1-ctd derived SER2 phosphorylated peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q94
- Type
- protein
- Length
- 282 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; RPB1-ctd
- UniProt
- Q9NQG5
- Ligands
- UNX, SO4, NH2
- Pockets
- 2 · best druggability 0.34
Structure
x-ray diffraction · 2 distinct chains · 74% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Regulation of nuclear pre-mRNA domain-containing protein 1B | protein | 129 | 81% helix, 1% strand | Q9NQG5 |
| C, D | RPB1-ctd | protein | 12 | 0% helix, 8% strand | — |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 19 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- NH2 · Amino group · ion · 2 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.34 | 0.75 | 14 | empty |
| 2 | 59 | 0.27 | 0.73 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1616 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 473 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 463 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 297 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 291 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified, 1 disulfide (phosphorylation, disulfide).
Compared structures
- 4Q94 · human RPRD1B CID in complex with a RPB1-CTD derived Ser2 phosphorylated peptide · 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 0.74
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 4Q94 · PDBe 4Q94 · UniProt Q9NQG5
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