Research workbench
Structure of human SCP1 bound to cis-proline peptidomimetic ctd phospho-SER5 peptide
Analyse Structure of human SCP1 bound to cis-proline peptidomimetic ctd phospho-SER5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YH1
- Type
- protein
- Length
- 366 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxy-terminal domain RNA polymerase II polypeptide a small phosphatase 1; A small…
- EC
- 3.1.3.16
- UniProt
- Q9GZU7
- Ligands
- MG
- Pockets
- 2 · best druggability 0.35
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Carboxy-terminal domain RNA polymerase II polypeptide a small phosphatase 1 (EC 3.1.3.16) | protein | 179 | 33% helix, 27% strand | Q9GZU7 |
| C, D | A small phosphatase 1 | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, C, B, 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 | 58 | 0.35 | 0.78 | 14 | MG |
| 2 | 50 | 0.30 | 0.76 | 14 | empty |
Interfaces
4 interfaces between chains.
- A–B · 583 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 398 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 376 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 55 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 4YH1 · Structure of Human Scp1 bound to cis-proline peptidomimetic CTD phospho-Ser5 peptide · the same entry in another collection · chain A against A, TM-score 1.00
- Q9GZU7 · AlphaFold monomer V2.0 prediction for carboxy-terminal domain RNA polymerase II… · a predicted model of the same protein · chain B against A, TM-score 1.00
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 Q9GZU7
- Elsewhere: RCSB PDB 4YH1 · PDBe 4YH1 · UniProt Q9GZU7
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