MolNFT v1 · #169399 · protein

Structure of cbl tyrosine kinase binding domain (tkbd) with C-terminal tail of src-like kinase protein 2 (SLAP2)

6XAR · E3 ubiquitin-protein ligase cbl: “Structure of cbl tyrosine kinase binding domain (tkbd) with C-terminal tail of src-like kinase protein 2…”. X-ray diffraction, 1 ligand (CA), 7 pockets (best druggability 0.82). MolNFT v1 #169399 on…

PDB: 6XAR
Type: protein
Length: 643 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase cbl; Src-like-adapter 2
EC: 2.3.2.27
UniProt: P22681
Ligands: CA
Pockets: 7 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 56% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	E3 ubiquitin-protein ligase cbl (EC 2.3.2.27)	protein	305	56% helix, 11% strand	P22681
B	E3 ubiquitin-protein ligase cbl (EC 2.3.2.27)	protein	300	56% helix, 9% strand	P22681
C, D	Src-like-adapter 2	protein	19	58% helix, 0% strand	—

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	811	0.82	0.85	100	empty
2	205	0.62	0.82	24	empty
3	93	0.53	0.84	20	empty
4	172	0.53	0.79	24	empty
5	90	0.53	0.84	18	empty

Interfaces

6 interfaces between chains.

B–D · 721 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 690 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 421 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 353 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 66 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6XAR · Structure of CBL tyrosine kinase binding domain (TKBD) with C-terminal tail of Src-like… · the same entry in another collection · chain A against A, TM-score 1.00
P22681 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase cbl (P22681) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 P22681
Elsewhere: RCSB PDB 6XAR · PDBe 6XAR · UniProt P22681

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