SMTL ID : 6o07.1

Structure and mechanism of acetylation by the N-terminal dual enzyme NatA/Naa50 complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-1-1-1-mer

Ligands

18 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 3 residues within 4Å: Chain A: P.132, Q.166, D.167 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain B: Y.511, K.515, K.551 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain B: Q.617 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain B: E.693, A.696 Ligand excluded by PLIP CL.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain B: E.443 Ligand excluded by PLIP CL.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: K.609, S.612 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: H.619, Y.722 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain B: R.708, E.709 Ligand excluded by PLIP CL.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.24: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.25: 1 residues within 4Å: Chain C: D.223 Ligand excluded by PLIP CL.26: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.27: 1 residues within 4Å: Chain B: L.285 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain C: N.158, A.161 Ligands: EPE.33 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain C: H.163, L.164, T.168 Ligand excluded by PLIP

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 1 residues within 4Å: Chain A: F.60 No protein-ligand interaction detected (PLIP) GOL.15: 9 residues within 4Å: Chain B: E.505, Y.508, R.509, E.610, K.613, E.848, Y.852, Y.853 Ligands: GOL.19 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.505, B:R.509, B:K.613, B:E.848 Water bridges: B:E.610, B:K.613 GOL.16: 3 residues within 4Å: Chain B: D.435, G.439, F.462 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.435 Water bridges: B:N.467, B:N.467, B:N.467 GOL.17: 2 residues within 4Å: Chain B: K.470, E.473 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.445, B:K.470, B:K.470 GOL.18: 2 residues within 4Å: Chain B: I.810, L.841 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.808 GOL.19: 6 residues within 4Å: Chain B: M.434, R.464, R.509, H.844, E.848 Ligands: GOL.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.509, B:E.848 GOL.30: 4 residues within 4Å: Chain C: H.114, T.116, H.153, Y.180 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.153, C:H.153 GOL.31: 5 residues within 4Å: Chain B: F.453 Chain C: A.19, H.22, T.84, M.121 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:N.23 Water bridges: B:K.457, B:K.457, B:K.457, B:K.457

1 x ACO: ACETYL COENZYME *A(Covalent)

ACO.3: 16 residues within 4Å: Chain A: E.94, F.95, L.96, G.97, V.98, R.103, H.104, K.105, S.106, I.107, G.108, S.109, Y.130, T.138, W.141, F.142 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.98, A:H.104, A:S.106, A:S.109, A:T.138 Water bridges: A:H.104

4 x MLI: MALONATE ION(Non-functional Binders)

MLI.20: 4 residues within 4Å: Chain B: L.431, P.843, Q.846, N.847 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.843 MLI.21: 3 residues within 4Å: Chain B: K.149, W.152, E.153 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:K.149, B:W.152 Hydrogen bonds: B:K.149, B:E.153 Salt bridges: B:K.149, B:K.149 MLI.22: 5 residues within 4Å: Chain B: H.201, L.205, D.232, I.233, C.236 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.205 Salt bridges: B:H.201 MLI.32: 7 residues within 4Å: Chain C: I.115, T.116, S.117, L.118, H.153, V.154, Y.165 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.118

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.23: 13 residues within 4Å: Chain B: S.346, K.349, I.422, R.426, K.429, H.430, K.457, K.460, Y.461, R.464 Chain C: K.80, Y.85, K.91 23 PLIP interactions: 19 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:S.346, B:Y.461 Water bridges: B:R.426 Salt bridges: B:K.349, B:K.349, B:R.426, B:R.426, B:R.426, B:R.426, B:K.429, B:K.429, B:K.429, B:H.430, B:K.457, B:K.457, B:K.457, B:K.460, B:K.460, B:R.464, C:K.80, C:K.91, C:K.91, C:K.91

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.33: 12 residues within 4Å: Chain C: V.120, Y.124, R.125, R.126, M.127, G.128, I.129, A.130, E.131, A.160, L.164 Ligands: CL.28 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:M.127, C:G.128, C:A.130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deng, S. et al., Structure and Mechanism of Acetylation by the N-Terminal Dual Enzyme NatA/Naa50 Complex. Structure (2019)

Release Date

2019-06-12

Peptides

N-terminal acetyltransferase A complex subunit NAT5: A
Naa15: B
N-terminal acetyltransferase A complex catalytic subunit ARD1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

N-terminal acetyltransferase A complex subunit NAT5

Naa15

N-terminal acetyltransferase A complex catalytic subunit ARD1

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