SMTL ID : 4kvm.4 (3 other biounits)

The NatA (Naa10p/Naa15p) amino-terminal acetyltransferase complex bound to a bisubstrate analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-mer

Ligands

1 x SER- ALA- SER- GLU: bisubstrate analog inhibitor(Non-covalent)

SER-ALA-SER-GLU.1: 7 residues within 4Å: Chain B: E.24, Y.26, T.74, H.111, Y.138, Y.139 Ligands: 1XE.19 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.26 Hydrogen bonds: B:E.24, B:T.74, B:Y.138, B:Y.138, B:Y.138, B:Y.139 Water bridges: B:Y.26

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

CL.2: 2 residues within 4Å: Chain A: F.535, R.539 Ligand excluded by PLIP CL.3: 1 residues within 4Å: Chain A: K.606 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Ligands: CL.12, CL.14 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: I.11, R.15 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain A: R.72 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: R.126, Y.128, K.129 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: R.146, V.182, E.186 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain A: R.159 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: K.201, D.202 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain A: K.324 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain A: R.422, K.453, K.456, Y.457 Ligands: CL.4 Ligand excluded by PLIP CL.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: K.425, R.460 Ligands: CL.4 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain A: R.448, W.494 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain A: K.508, A.510, L.511 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain B: K.29 Ligand excluded by PLIP

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

SO4.17: 5 residues within 4Å: Chain A: R.221, L.225, L.247, R.251 Chain B: R.97 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.97 Salt bridges: A:R.221, A:R.251

1 x 1XE: [5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)furan-2-yl]methyl (3R)-4-{[3-({(E)-2-[(2,2-dihydroxyethyl)sulfanyl]ethenyl}amino)-3-oxopropyl]amino}-3-hydroxy-2,2-dimethyl-4-oxobutyl dihydrogen diphosphate(Non-covalent)

1XE.19: 23 residues within 4Å: Chain B: N.21, L.22, S.75, V.76, S.77, V.78, R.83, H.84, G.86, L.87, A.88, K.89, H.111, V.112, N.116, R.117, A.118, A.119, H.121, L.122, Y.123, T.126 Ligands: SER-ALA-SER-GLU.1 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.22 Hydrogen bonds: B:V.76, B:V.76, B:V.78, B:V.78, B:H.84, B:L.85, B:G.86, B:L.87, B:A.88, B:K.89, B:N.116, B:R.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liszczak, G. et al., Molecular basis for N-terminal acetylation by the heterodimeric NatA complex. Nat.Struct.Mol.Biol. (2013)

Release Date

2013-07-31

Peptides

N-terminal acetyltransferase A complex subunit nat1: A
N-terminal acetyltransferase A complex catalytic subunit ard1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
H

N-terminal acetyltransferase A complex subunit nat1

N-terminal acetyltransferase A complex catalytic subunit ard1

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