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Structure of gak kinase in complex with nanobody (NBGAK_4)

Analyse Structure of gak kinase in complex with nanobody (NBGAK_4) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4C59
Type: protein
Length: 387 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyclin-G-associated kinase; Nanobody
EC: 2.7.11.1
UniProt: O14976
Ligands: FEF
Pockets: 3 · best druggability 0.64

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyclin-G-associated kinase (EC 2.7.11.1)	protein	266	36% helix, 21% strand	O14976
B	Nanobody	protein	121	8% helix, 50% strand	—

Ligands and binding sites

FEF · (2Z,3E)-2,3'-biindole-2',3(1H,1'H)-dione 3-{O-[(3R)-3,4-dihydroxybutyl]oxime} · ligand · chains A

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

Pockets

3 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	490	0.64	0.77	51	empty
2	305	0.64	0.80	37	FEF
3	57	0.43	0.82	14	empty

Interfaces

1 interface between chains.

A–B · 620 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

4C59 · Structure of GAK kinase in complex with nanobody (NbGAK_4) · the same entry in another collection · chain A against A, TM-score 1.00
O14976 · AlphaFold monomer V2.0 prediction for cyclin-G-associated kinase (O14976) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 O14976
Elsewhere: RCSB PDB 4C59 · PDBe 4C59 · UniProt O14976

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