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Ctd-specific phosphatase SCP1 in complex with peptide from C-terminal domain of RNA polymerase II

Analyse Ctd-specific phosphatase SCP1 in complex with peptide from C-terminal domain of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2GHT
Type: protein
Length: 373 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; DNA-directed…
EC: 3.1.3.16, 2.7.7.6
UniProt: Q9GZU7, P24928
Ligands: MG

Structure

x-ray diffraction · 3 distinct chains · 28% helix, 24% 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	180	30% helix, 26% strand	Q9GZU7
C	DNA-directed RNA polymerase II largest subunit (EC 2.7.7.6)	protein	5	0% helix, 0% strand	P24928
D	DNA-directed RNA polymerase II largest subunit (EC 2.7.7.6)	protein	8	0% helix, 0% strand	P24928

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.

Interfaces

4 interfaces between chains.

B–D · 632 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 558 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 377 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 55 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (phosphorylation).

Compared structures

2GHT · CTD-specific phosphatase Scp1 in complex with peptide from C-terminal domain of RNA… · the same entry in another collection · chain D against D, 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 0.99
P24928 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase II subunit RPB1 (P24928) · a predicted model of the same protein · chain C against A, TM-score 0.77

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
Every structure of UniProt P24928
Elsewhere: RCSB PDB 2GHT · PDBe 2GHT · UniProt Q9GZU7 · UniProt P24928

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