SMTL ID : 6ppl.1

Cryo-EM structure of human NatE complex (NatA/Naa50)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

2 x ACO: ACETYL COENZYME *A(Covalent)

ACO.1: 20 residues within 4Å: Chain A: I.26, F.27, L.77, G.78, C.79, R.84, R.85, L.86, G.87, I.88, G.89, T.90, H.112, V.113, Q.114, N.117, S.119, A.120, F.123, K.126 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.26, A:V.113, A:Q.114, A:F.123 Hydrogen bonds: A:L.77, A:R.85, A:R.85, A:R.85, A:G.87, A:I.88, A:G.89, A:T.90, A:T.90, A:N.117, A:S.119 Salt bridges: A:R.85 pi-Cation interactions: A:R.85, A:R.85 ACO.3: 23 residues within 4Å: Chain A: D.53 Chain C: L.23, T.74, S.75, L.76, A.77, V.78, R.83, R.84, L.85, G.86, L.87, A.88, Q.89, H.111, N.116, R.117, A.118, A.119, H.121, L.122, Y.123, T.126 18 PLIP interactions: 17 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:L.76 Hydrogen bonds: C:V.78, C:R.84, C:R.84, C:L.85, C:G.86, C:A.88, C:Q.89, C:Q.89, C:N.116, C:R.117, C:H.121, C:Y.123, C:T.126 Salt bridges: C:R.84, B:K.320 pi-Cation interactions: C:R.84, C:R.84

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.2: 11 residues within 4Å: Chain B: K.416, K.419, H.420, K.447, K.450, Y.451, K.556 Chain C: H.17, K.52, K.79, S.81 21 PLIP interactions: 14 interactions with chain B, 7 interactions with chain C Hydrogen bonds: B:Y.451, C:S.81 Salt bridges: B:K.416, B:K.416, B:K.416, B:K.419, B:K.419, B:H.420, B:K.447, B:K.447, B:K.447, B:K.450, B:K.450, B:K.450, B:K.556, C:H.17, C:K.52, C:K.52, C:K.52, C:K.79, C:K.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deng, S. et al., Molecular basis for N-terminal acetylation by human NatE and its modulation by HYPK. Nat Commun (2020)

Release Date

2020-02-19

Peptides

N-alpha-acetyltransferase 50: A
N-alpha-acetyltransferase 15, NatA auxiliary subunit: B
N-alpha-acetyltransferase 10: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

N-alpha-acetyltransferase 50

N-alpha-acetyltransferase 15, NatA auxiliary subunit

N-alpha-acetyltransferase 10

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