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Structure of SCP1 D96N bound to rest-PS861/4 peptide

Analyse Structure of SCP1 D96N bound to rest-PS861/4 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6DU3
Type: protein
Length: 372 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; Rest-PS861
EC: 3.1.3.16
UniProt: Q9GZU7
Ligands: MG
Pockets: 3 · best druggability 0.38

Structure

x-ray diffraction · 3 distinct chains · 28% helix, 26% 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, 27% strand	Q9GZU7
C	Rest-PS861	protein	7	0% helix, 0% strand	—
D	Rest-PS861	protein	5	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

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	53	0.38	0.79	12	empty
2	53	0.30	0.76	18	empty
3	72	0.29	0.73	17	empty

Interfaces

3 interfaces between chains.

A–B · 568 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 450 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 411 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (phosphorylation).

Compared structures

6DU3 · Structure of Scp1 D96N bound to REST-pS861/4 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 A against A, TM-score 0.99

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 6DU3 · PDBe 6DU3 · UniProt Q9GZU7

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