SMTL ID : 4xpd.1

Crystal structure of yeast N-terminal acetyltransferase NatE (ppGpp) in complex with a bisubstrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.81 Å

Oligo State

hetero-oligomer

Ligands

1 x SER- TYR- SER- MET- GLU- HIS: human ACTH8(Non-covalent)

SER-TYR-SER-MET-GLU-HIS.1: 11 residues within 4Å: Chain A: K.480 Chain B: L.24, E.26, Y.28, Y.32, T.116, H.153, Y.180, Y.181, Q.182 Ligands: CMC.4 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.28, B:T.116, B:Q.182 Hydrogen bonds: B:E.26, B:Y.28, B:T.116, B:Y.180, B:Y.180, B:Y.181 Salt bridges: A:K.480

1 x G4P: GUANOSINE-5',3'-TETRAPHOSPHATE(Non-covalent)

G4P.2: 10 residues within 4Å: Chain A: K.349, Q.353, R.426, K.429, K.457, K.460, Y.461 Chain B: P.83, Y.85, K.91 17 PLIP interactions: 5 interactions with chain B, 12 interactions with chain A Hydrogen bonds: B:Y.85, B:K.91, B:K.91, B:K.91, A:K.349, A:Q.353, A:Y.461 Salt bridges: B:K.91, A:K.429, A:K.429, A:K.457, A:K.460, A:K.460, A:K.460, A:K.460 pi-Cation interactions: A:K.349, A:K.349

1 x ACO: ACETYL COENZYME *A(Non-covalent)

ACO.3: 22 residues within 4Å: Chain C: T.26, V.27, L.30, Y.31, I.93, E.94, F.95, L.96, V.98, R.103, H.104, K.105, S.106, I.107, G.108, S.109, V.129, Y.130, L.131, W.141, A.144, H.145 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:L.30, C:L.96, C:W.141 Hydrogen bonds: C:L.96, C:V.98, C:R.103, C:H.104, C:K.105, C:S.106, C:I.107, C:G.108, C:S.109

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

CMC.4: 26 residues within 4Å: Chain B: N.23, L.24, T.116, S.117, L.118, S.119, V.120, R.125, R.126, M.127, G.128, I.129, A.130, E.131, L.152, H.153, V.154, N.158, A.160, A.161, H.163, L.164, Y.165, T.168 Chain C: E.68 Ligands: SER-TYR-SER-MET-GLU-HIS.1 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.24, B:L.118, B:A.130 Hydrogen bonds: B:L.118, B:L.118, B:V.120, B:R.125, B:R.126, B:R.126, B:M.127, B:G.128, B:I.129, B:A.130, B:E.131, B:N.158, B:R.159, C:E.68 Salt bridges: B:H.163 pi-Cation interactions: B:R.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, J. et al., Crystal structure of yeast N-terminal acetyltransferase NatE (ppGpp) in complex with a bisubstrate. To Be Published

Release Date

2016-07-20

Peptides

N-terminal acetyltransferase A complex subunit NAT1: A
N-terminal acetyltransferase A complex catalytic subunit ARD1: B
N-terminal acetyltransferase A complex subunit NAT5: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

N-terminal acetyltransferase A complex subunit NAT1

N-terminal acetyltransferase A complex catalytic subunit ARD1

N-terminal acetyltransferase A complex subunit NAT5

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