SMTL ID : 7ztl.1

Crystal structure of a covalently linked Aurora-A N-Myc complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 21 residues within 4Å: Chain A: L.45, G.46, K.47, G.48, K.49, V.53, A.66, K.68, L.100, L.116, E.117, Y.118, A.119, T.123, E.166, N.167, L.169, D.180 Ligands: MG.2, MG.3, BCN.6 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:K.49, A:E.117, A:A.119 Water bridges: A:K.47, A:K.47, A:G.51, A:T.123, A:T.123, A:E.166, A:N.167, A:D.180 Salt bridges: A:K.68, A:K.68

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: K.68, D.180 Ligands: ADP.1, BCN.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.180, A:D.180 MG.3: 4 residues within 4Å: Chain A: N.167, D.180 Ligands: ADP.1, BCN.6 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.180, H2O.2, H2O.4

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: D.200, A.237, N.238, T.239, Y.240, T.243 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.239 Water bridges: A:D.200, A:D.200, A:D.200, A:A.237, A:T.243 GOL.5: 4 residues within 4Å: Chain A: Y.226, V.230, T.253, P.255 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.253, A:T.253 Water bridges: A:T.253 GOL.7: 3 residues within 4Å: Chain A: E.76, G.79, E.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.79, A:E.81

1 x BCN: BICINE(Non-covalent)

BCN.6: 11 residues within 4Å: Chain A: K.49, F.50, K.68, Q.83, E.87, D.180, G.182, W.183 Ligands: ADP.1, MG.2, MG.3 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:K.68, A:E.87, A:G.182 Water bridges: A:K.49, A:K.164, A:K.164, A:K.164, A:K.164, A:N.167, A:W.183, A:W.183 Salt bridges: A:E.87, A:K.164, A:D.180

1 x NA: SODIUM ION(Non-functional Binders)

NA.8: 1 residues within 4Å: Chain A: E.236 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.236

1 x JWG: 4-(3-hydroxy-3-oxopropylamino)-4-oxidanylidene-butanoic acid(Covalent)

JWG.9: 4 residues within 4Å: Chain A: Q.241, C.245, R.249 Chain B: K.58 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.249 Salt bridges: A:R.249

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diebold, M. et al., Crystal structure of a covalently linked Aurora-A-MYCN complex. Acta Crystallogr D Struct Biol (2023)

Release Date

2023-01-18

Peptides

Aurora kinase A: A
N-myc proto-oncogene protein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aurora kinase A

N-myc proto-oncogene protein