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Crystal structure of CBLN1 (VAL55-GLY58 deletion mutant)

Analyse Crystal structure of CBLN1 (VAL55-GLY58 deletion mutant) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5KC6
Type: protein
Length: 417 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cerebellin-1
UniProt: P23435
Ligands: NAG
Pockets: 7 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 4% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cerebellin-1	protein	137	4% helix, 52% strand	P23435
B	Cerebellin-1	protein	144	4% helix, 49% strand	P23435
C	Cerebellin-1	protein	136	4% helix, 52% strand	P23435

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B, C

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

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	301	0.76	0.88	51	empty
2	59	0.71	0.98	27	empty
3	134	0.47	0.77	21	empty
4	54	0.46	0.84	13	empty
5	54	0.45	0.84	13	empty

Interfaces

3 interfaces between chains.

B–C · 845 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 828 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 811 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 glycan (N-glycosylation).

Compared structures

5KC6 · Crystal structure of Cbln1 (Val55-Gly58 deletion mutant) · the same entry in another collection · chain A against A, TM-score 1.00
P23435 · AlphaFold monomer V2.0 prediction for cerebellin-1 (P23435) · a predicted model of the same protein · chain C against A, TM-score 0.96

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 P23435
Elsewhere: RCSB PDB 5KC6 · PDBe 5KC6 · UniProt P23435

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