SMTL ID : 7kpu.2 (1 other biounit)

Crystal structure of human NatD (NAA40) bound to a bisubstrate analogue with a C-3 linker

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

monomer

Ligands

1 x SER- GLY- ARG- GLY- LYS: bisubstrate analogue (CMC-ACE-SER-GLY-ARG-GLY-LYS)(Non-covalent)

SER-GLY-ARG-GLY-LYS.1: 24 residues within 4Å: Chain A: T.61, M.65, Y.69, W.74, K.81, E.84, R.109, D.111, V.112, E.113, Y.120, Y.122, E.123, Q.125, T.158, V.159, F.160, S.181, P.183, Y.195, I.197 Ligands: WZG.8, NH2.9, ACE.10 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: 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:Y.195, A:Y.195 Water bridges: A:E.113, A:E.113, A:Y.120, A:T.158, A:T.158 Salt bridges: A:D.111, A:E.113

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

SO4.2: 3 residues within 4Å: Chain A: Y.167, R.171, I.178 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.167 Water bridges: A:E.196, A:E.196 Salt bridges: A:R.171 SO4.4: 2 residues within 4Å: Chain A: R.131 Ligands: WZG.8 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.131 SO4.5: 1 residues within 4Å: Chain A: R.79 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.79

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: V.28, F.29, K.31, Y.32, D.33, R.34, F.138 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.31, A:D.33, A:R.34 Water bridges: A:K.31 GOL.6: 4 residues within 4Å: Chain A: K.161, P.183, S.184, C.193 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.161 Water bridges: A:S.184, A:S.184, A:C.193, A:C.193, A:E.196 GOL.7: 5 residues within 4Å: Chain A: E.42, K.44, W.96, S.99, S.100 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.99 Water bridges: A:E.42, A:K.44

1 x WZG: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (3R)-3-hydroxy-2,2-dimethyl-4-[(3-{[2-(methylsulfanyl)ethyl]amino}-3-oxopropyl)amino]-4-oxobutyl dihydrogen diphosphate (non-preferred name)(Non-covalent)

WZG.8: 25 residues within 4Å: Chain A: N.64, M.65, M.68, V.124, Q.125, L.126, R.131, R.132, K.133, G.134, L.135, G.136, K.137, L.157, V.159, N.163, G.165, A.166, Q.168, F.169, F.170, A.173 Ligands: SER-GLY-ARG-GLY-LYS.1, SO4.4, ACE.10 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:V.124, A:A.166 Hydrogen bonds: A:V.124, A:L.126, A:R.131, A:R.132, A:R.132, A:G.134, A:G.134, A:L.135, A:G.136, A:K.137, A:N.163 Water bridges: A:K.133, A:K.133, A:K.137, A:G.165, A:G.165 Salt bridges: A:R.132 pi-Cation interactions: A:R.132, A:R.132

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

NH2.9: 6 residues within 4Å: Chain A: S.181, S.182, P.183, 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

1 x ACE: ACETYL GROUP(Non-functional Binders)

ACE.10: 11 residues within 4Å: Chain A: C.121, Y.122, E.123, V.124, Q.125, L.157, T.158, V.159, F.170 Ligands: SER-GLY-ARG-GLY-LYS.1, WZG.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.157 Hydrogen bonds: A:V.124, A:Q.125

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
A

N-alpha-acetyltransferase 40

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