Research workbench
Cid of human RPRD1B in complex with an unmodified ctd peptide
Analyse Cid of human RPRD1B in complex with an unmodified ctd peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q96
- Type
- protein
- Length
- 551 residues
- Chains
- 6
- 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
- BTN, UNX, SO4, NH2
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 75% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Regulation of nuclear pre-mRNA domain-containing protein 1B | protein | 129 | 79% helix, 1% strand | Q9NQG5 |
| B, D | Regulation of nuclear pre-mRNA domain-containing protein 1B | protein | 128 | 80% helix, 1% strand | Q9NQG5 |
| C, F | RPB1-ctd | protein | 19 | 0% helix, 5% strand | — |
| E | Regulation of nuclear pre-mRNA domain-containing protein 1B | protein | 128 | 79% helix, 1% strand | Q9NQG5 |
Ligands and binding sites
- BTN · Biotin · ligand · 2 copies · chains B, C, E, F
- UNX · Unknown atom or ion · ion · 23 copies · chains A, C, D, B, F, E
- SO4 · Sulfate ion · ion · 4 copies · chains B, F, A, D, E
- NH2 · Amino group · ion · 2 copies · chains B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.61 | 0.75 | 53 | BTN, SO4 |
| 2 | 246 | 0.60 | 0.80 | 26 | empty |
| 3 | 446 | 0.59 | 0.75 | 44 | BTN, UNX |
| 4 | 231 | 0.55 | 0.78 | 28 | UNX |
Interfaces
13 interfaces between chains.
- A–B · 1666 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1651 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 689 Ų buried · 8 hydrogen bonds · protein-protein
- C–E · 681 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 492 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor, 2 disulfide (biotinylation, disulfide).
Compared structures
- 4Q96 · CID of human RPRD1B in complex with an unmodified CTD peptide · the same entry in another collection · chain F against F, 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 E 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 4Q96 · PDBe 4Q96 · UniProt Q9NQG5
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