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Crystal complex of sys-1/POP-1 at 2.5A resolution

Analyse Crystal complex of sys-1/POP-1 at 2.5A resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3C2G
Type: protein
Length: 1,249 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sys-1 protein; Pop-1 8-residue peptide
UniProt: Q9XVI2, Q10666
Pockets: 10 · best druggability 0.40

Structure

x-ray diffraction · 3 distinct chains · 70% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sys-1 protein	protein	618	70% helix, 0% strand	Q9XVI2
B	Sys-1 protein	protein	615	70% helix, 0% strand	Q9XVI2
C, D	Pop-1 8-residue peptide	protein	8	0% helix, 0% strand	Q10666

Pockets

10 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	154	0.40	0.73	24	empty
2	71	0.39	0.79	17	empty
3	76	0.39	0.78	24	empty
4	72	0.36	0.76	13	empty
5	83	0.35	0.75	17	empty

Interfaces

3 interfaces between chains.

A–B · 842 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 655 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 616 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 30 modified (engineered).

Compared structures

3C2G · Crystal complex of SYS-1/POP-1 at 2.5A resolution · the same entry in another collection · chain A against A, TM-score 1.00
Q10666 · AlphaFold monomer V2.0 prediction for protein pop-1 (Q10666) · a predicted model of the same protein · chain C against A, TM-score 0.63

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 Q9XVI2
Every structure of UniProt Q10666
Elsewhere: RCSB PDB 3C2G · PDBe 3C2G · UniProt Q9XVI2 · UniProt Q10666

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