SMTL ID : 4u9w.2 (3 other biounits)

Crystal Structure of NatD bound to H4/H2A peptide and CoA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

monomer

Ligands

1 x SER- GLY- ARG- GLY- LYS- NH2: Histone H4/H2A N-terminus(Non-covalent)

SER-GLY-ARG-GLY-LYS-NH2.1: 17 residues within 4Å: Chain A: M.68, Y.72, W.77, K.84, D.114, V.115, E.116, Y.123, Y.125, E.126, T.161, S.184, P.186, Y.198, I.200 Ligands: COA.2, NA.3 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:Y.123 Hydrogen bonds: A:K.84, A:V.115, A:Y.125, A:Y.125, A:Y.125, A:E.126, A:T.161, A:T.161, A:S.184, A:Y.198, A:Y.198 Water bridges: A:E.87, A:R.112, A:E.116, A:T.161, A:T.161, A:S.184 Salt bridges: A:D.114, A:E.116 pi-Cation interactions: A:Y.123

1 x COA: COENZYME A(Non-covalent)

COA.2: 22 residues within 4Å: Chain A: N.67, M.68, V.127, Q.128, L.129, R.134, R.135, K.136, G.137, L.138, G.139, K.140, T.161, N.166, G.168, A.169, Q.171, F.172, F.173, A.176 Ligands: SER-GLY-ARG-GLY-LYS-NH2.1, NA.3 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:V.127 Hydrogen bonds: A:V.127, A:Q.128, A:L.129, A:R.135, A:R.135, A:K.136, A:G.137, A:G.137, A:L.138, A:G.139, A:K.140, A:N.166 Water bridges: A:V.133, A:R.135, A:R.135, A:R.135 Salt bridges: A:R.135 pi-Cation interactions: A:R.135, A:R.135

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain A: E.126, V.127 Ligands: SER-GLY-ARG-GLY-LYS-NH2.1, COA.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.126, A:V.127, A:Q.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Magin, R.S. et al., The Molecular Basis for Histone H4- and H2A-Specific Amino-Terminal Acetylation by NatD. Structure (2015)

Release Date

2015-01-28

Peptides

N-alpha-acetyltransferase 40: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

N-alpha-acetyltransferase 40

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