MolNFT v1 · #126810 · protein

Structure of the SCC2 C-terminus

5ME3 · Sister chromatid cohesion protein 2: “Structure of the SCC2 C-terminus”. X-ray diffraction, 20 pockets (best druggability 0.70). MolNFT v1 #126810 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ME3
Type: protein
Length: 1,988 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sister chromatid cohesion protein 2; Unassigned sequence of SCC2; SCC2 unassigned sequence
UniProt: Q750S2
Pockets: 20 · best druggability 0.70

Structure

x-ray diffraction · 5 distinct chains · 75% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sister chromatid cohesion protein 2	protein	973	74% helix, 1% strand	Q750S2
B	Sister chromatid cohesion protein 2	protein	960	75% helix, 0% strand	Q750S2
X, Y	Unassigned sequence of SCC2	protein	17	88% helix, 0% strand	—
Z	SCC2 unassigned sequence	protein	11	82% helix, 0% strand	—
W	SCC2 unassigned sequence	protein	10	80% helix, 0% strand	—

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	936	0.70	0.75	107	empty
2	193	0.64	0.84	33	empty
3	520	0.64	0.76	59	empty
4	192	0.61	0.83	33	empty
5	96	0.59	0.86	22	empty

Interfaces

7 interfaces between chains.

A–B · 876 Å² buried · 6 hydrogen bonds · protein-protein
A–X · 268 Å² buried · 0 hydrogen bonds · protein-protein
B–Y · 242 Å² buried · 0 hydrogen bonds · protein-protein
A–Z · 169 Å² buried · 0 hydrogen bonds · protein-protein
B–W · 115 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5ME3 · Structure of the Scc2 C-terminus · the same entry in another collection · chain W against W, TM-score 1.00
Q750S2 · AlphaFold monomer V2.0 prediction for sister chromatid cohesion protein 2 (Q750S2) · a predicted model of the same protein · chain A against A, TM-score 0.79

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 Q750S2
Elsewhere: RCSB PDB 5ME3 · PDBe 5ME3 · UniProt Q750S2

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