SMTL ID : 4xnh.1

Crystal structure of yeast N-terminal acetyltransferase NatE (IP6) in complex with a bisubstrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x SER- TYR- SER- MET- GLU- HIS: ACYH8(Non-covalent)

SER-TYR-SER-MET-GLU-HIS.1: 12 residues within 4Å: Chain A: K.480 Chain B: L.24, E.26, Y.28, Y.32, T.116, S.117, H.153, Y.180, Y.181, Q.182 Ligands: CMC.4 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.28 Hydrogen bonds: B:E.26, B:Y.28, B:T.116, B:T.116, B:Y.180, B:Y.181 Water bridges: B:H.153, B:H.153, B:Y.180 Salt bridges: A:K.480

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.2: 17 residues within 4Å: Chain A: S.346, K.349, Q.353, I.422, R.426, K.429, H.430, F.453, K.457, K.460, Y.461, R.464 Chain B: K.80, Y.85, K.91, T.123, Y.124 35 PLIP interactions: 26 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:S.346, A:Y.461, B:Y.85, B:T.123, B:Y.124 Water bridges: A:K.349, A:R.426, A:R.426, A:R.426, A:R.426, A:R.426, A:R.426, A:R.426, A:R.426, B:K.80, B:K.80 Salt bridges: A:K.349, A:K.349, A:K.349, A:R.426, A:R.426, A:R.426, A:K.429, A:K.429, A:K.429, A:H.430, A:K.457, A:K.457, A:K.460, A:K.460, A:R.464, B:K.80, B:K.80, B:K.91, B:K.91

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

ACO.3: 27 residues within 4Å: Chain C: T.26, V.27, L.30, Y.31, I.93, E.94, F.95, L.96, G.97, V.98, R.103, H.104, K.105, S.106, I.107, G.108, S.109, V.129, Y.130, L.131, P.132, D.135, T.138, W.141, F.142, A.144, H.145 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:V.27, C:L.96 Hydrogen bonds: C:L.96, C:L.96, C:V.98, C:R.103, C:R.103, C:H.104, C:H.104, C:K.105, C:S.106, C:I.107, C:G.108, C:S.109, C:S.109, C:W.141 Water bridges: C:T.138

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

CMC.4: 28 residues within 4Å: Chain A: D.451 Chain B: N.23, L.24, 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, R.159, A.160, A.161, H.163, L.164, Y.165, T.168, R.207 Chain C: E.68 Ligands: SER-TYR-SER-MET-GLU-HIS.1 27 PLIP interactions: 25 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:L.24, B:L.118, B:A.130, B:A.161 Hydrogen bonds: B:L.118, B:L.118, B:V.120, B:R.126, B:R.126, B:M.127, B:G.128, B:G.128, B:I.129, B:A.130, B:E.131, B:N.158, B:H.163, B:T.168, B:T.168, C:E.68 Water bridges: B:R.125, B:R.159, B:R.159, C:E.68 Salt bridges: B:H.163, B:R.207 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 (IP6) 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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