MolNFT v1 · #125424 · protein

Aurora-a kinase domain in complex with vnar-D01 S93R

5L8J · Aurora kinase a: “Aurora-a kinase domain in complex with vnar-D01 S93R”. X-ray diffraction, 1 ligand (ADP), 3 pockets (best druggability 0.60). MolNFT v1 #125424 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5L8J
Type: protein
Length: 358 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aurora kinase a; New antigen receptor variable domain
EC: 2.7.11.1
UniProt: O14965, Q8JJ25
Ligands: ADP
Pockets: 3 · best druggability 0.60

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Aurora kinase a (EC 2.7.11.1)	protein	253	43% helix, 18% strand	O14965
B	New antigen receptor variable domain	protein	105	3% helix, 51% strand	Q8JJ25

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains A
EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
PEG · Di(hydroxyethyl)ether · additive · 2 copies · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	359	0.60	0.77	33	ADP
2	91	0.34	0.74	15	EDO
3	80	0.34	0.75	17	empty

Interfaces

1 interface between chains.

A–B · 891 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5L8J · Aurora-A kinase domain in complex with vNAR-D01 S93R · the same entry in another collection · chain B against B, TM-score 1.00
O14965 · AlphaFold monomer V2.0 prediction for aurora kinase a (O14965) · a predicted model of the same protein · chain A 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 O14965
Every structure of UniProt Q8JJ25
Elsewhere: RCSB PDB 5L8J · PDBe 5L8J · UniProt O14965 · UniProt Q8JJ25

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