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

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

Coordinates

PDB Format

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, E.87, D.114, V.115, E.116, Y.123, Y.125, E.126, T.161, Y.198, I.200 Ligands: COA.2, NA.3, GOL.4 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.123, A:Y.125 Hydrogen bonds: A:Y.72, A:K.84, A:V.115, A:Y.125, A:Y.125, A:E.126, A:T.161, A:T.161, A:T.161, A:T.161, A:Y.198, A:Y.198 Water bridges: A:E.116, A:F.163, A:S.184 Salt bridges: A:D.114, A:E.116

1 x COA: COENZYME A(Non-covalent)

COA.2: 20 residues within 4Å: Chain A: 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 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:V.127, A:F.172 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: 6 residues within 4Å: Chain A: Y.125, E.126, V.127, Q.128 Ligands: SER-GLY-ARG-GLY-LYS-NH2.1, COA.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.127, A:V.127, A:Q.128

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: Y.72, W.77, K.84, E.87 Ligands: SER-GLY-ARG-GLY-LYS-NH2.1, SER-GLY-ARG-GLY-LYS-NH2.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.77, A:K.84, A:E.87

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
C

N-alpha-acetyltransferase 40

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