SMTL ID : 7kd7.1 (1 other biounit)

Crystal structure of human NatD (NAA40) bound to a bisubstrate analogue

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.44 Å

Oligo State

monomer

Ligands

1 x SER- GLY- ARG- GLY- LYS: SER-GLY-ARG-GLY-LYS(Non-covalent)

SER-GLY-ARG-GLY-LYS.1: 21 residues within 4Å: Chain A: T.61, M.65, Y.69, W.74, K.81, E.84, D.111, V.112, E.113, Y.120, Y.122, E.123, Q.125, T.158, V.159, F.160, P.183, Y.195, I.197 Ligands: CMC.8, NH2.9 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:Y.120, A:Y.120, A:Y.122 Hydrogen bonds: A:Y.69, A:K.81, A:V.112, A:Y.122, A:Y.122, A:E.123, A:Q.125, A:T.158, A:T.158, A:T.158, A:T.158, A:Y.195, A:Y.195 Water bridges: A:E.84, A:E.113, A:E.113, A:Y.120 Salt bridges: A:D.111, A:E.113

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: Q.144, N.148, R.200, T.202 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.144, A:N.148, A:R.200 GOL.3: 7 residues within 4Å: Chain A: T.63, N.64, M.65, M.68, S.128, R.131 Ligands: CMC.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.64, A:N.64, A:R.131, A:R.131

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 2 residues within 4Å: Chain A: R.132 Ligands: CMC.8 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.132 SO4.5: 3 residues within 4Å: Chain A: K.62, Q.66 Ligands: BTB.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.66 Salt bridges: A:K.62 SO4.6: 3 residues within 4Å: Chain A: Y.167, R.171, I.178 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.167 Salt bridges: A:R.171

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.7: 2 residues within 4Å: Chain A: Q.66 Ligands: SO4.5 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.67, A:T.67

1 x CMC: CARBOXYMETHYL COENZYME *A(Non-covalent)

CMC.8: 28 residues within 4Å: Chain A: N.64, M.65, M.68, Y.122, E.123, V.124, Q.125, L.126, R.131, R.132, K.133, G.134, L.135, G.136, K.137, L.157, T.158, V.159, N.163, G.165, A.166, Q.168, F.169, F.170, A.173 Ligands: SER-GLY-ARG-GLY-LYS.1, GOL.3, SO4.4 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:A.166 Hydrogen bonds: A:E.123, A:V.124, A:V.124, A:Q.125, A:L.126, A:R.131, A:R.132, A:R.132, A:K.133, A:G.134, A:L.135, A:G.136, A:K.137, A:N.163 Water bridges: A:V.130, A:R.132, A:K.137, A:A.166 Salt bridges: A:R.132, A:K.137 pi-Cation interactions: A:R.132, A:R.132

1 x NH2: AMINO GROUP(Non-functional Binders)

NH2.9: 7 residues within 4Å: Chain A: S.181, S.182, P.183, Y.195, I.197 Ligands: SER-GLY-ARG-GLY-LYS.1, SER-GLY-ARG-GLY-LYS.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deng, Y. et al., Novel Bisubstrate Inhibitors for Protein N-Terminal Acetyltransferase D. J.Med.Chem. (2021)

Release Date

2021-06-16

Peptides

N-alpha-acetyltransferase 40: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

N-alpha-acetyltransferase 40

Related Entries With Identical Sequence