MolNFT v1 · #78627 · protein

Structure of CASKIN1 tandem sams

3SEN · Caskin-1: “Structure of CASKIN1 tandem sams”. X-ray diffraction, 1 ligand (K), 4 pockets (best druggability 0.65). MolNFT v1 #78627 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3SEN
Type: protein
Length: 554 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caskin-1
UniProt: Q8WXD9
Ligands: K
Pockets: 4 · best druggability 0.65

Structure

x-ray diffraction · 4 distinct chains · 63% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Caskin-1	protein	142	65% helix, 0% strand	Q8WXD9
B	Caskin-1	protein	139	66% helix, 0% strand	Q8WXD9
C	Caskin-1	protein	136	62% helix, 0% strand	Q8WXD9
D	Caskin-1	protein	137	61% helix, 0% strand	Q8WXD9

Ligands and binding sites

K · Potassium ion · metal · chains A, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	637	0.65	0.75	70	K
2	79	0.40	0.78	18	empty
3	53	0.32	0.77	9	empty
4	52	0.28	0.74	10	empty

Interfaces

4 interfaces between chains.

A–D · 449 Å² buried · 1 hydrogen bond · protein-protein
A–B · 445 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 392 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 30 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3SEN · Structure of Caskin1 Tandem SAMs · the same entry in another collection · chain D against D, TM-score 1.00
Q8WXD9 · AlphaFold monomer V2.0 prediction for caskin-1 (Q8WXD9) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 Q8WXD9
Elsewhere: RCSB PDB 3SEN · PDBe 3SEN · UniProt Q8WXD9

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