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Crystal structure of human SCP1 bound to trans-proline peptidomimetic ctd phospho-SER5 peptide

Analyse Crystal structure of human SCP1 bound to trans-proline peptidomimetic ctd… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4YGY
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…
EC: 3.1.3.16
UniProt: Q9GZU7
Ligands: MG
Pockets: 2 · best druggability 0.32

Structure

x-ray diffraction · 2 distinct chains · 31% 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	32% helix, 27% strand	Q9GZU7
C, D	Peptidomimetic ctd phospho-SER5 peptide	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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	51	0.32	0.78	12	empty
2	51	0.32	0.78	18	empty

Interfaces

4 interfaces between chains.

A–B · 577 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 404 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 397 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 50 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (nonstandard).

Compared structures

4YGY · Crystal Structure of Human Scp1 bound to trans-proline peptidomimetic CTD phospho-Ser5… · 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 4YGY · PDBe 4YGY · UniProt Q9GZU7

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