SMTL ID : 6ygb.1

Crystal structure of the NatC complex bound to CoA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x COA: COENZYME A(Non-covalent)

COA.1: 16 residues within 4Å: Chain A: L.84, A.85, V.86, R.91, G.92, H.93, G.94, I.95, A.96, K.97, E.118, N.123, A.125, N.128, L.129, Y.130 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.84, A:A.96 Hydrogen bonds: A:L.84, A:V.86, A:G.92, A:G.94, A:I.95, A:A.96, A:K.97, A:N.123, A:N.128

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

CL.2: 2 residues within 4Å: Chain A: S.18, I.60 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain B: N.385, S.432 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain B: P.269, A.272, F.273 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain B: H.367, W.438 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain B: N.694 Ligand excluded by PLIP CL.19: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain B: E.370, Q.530, A.533 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain B: H.498, M.528, Q.532 Ligand excluded by PLIP

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 6 residues within 4Å: Chain A: H.72, R.73, R.78, K.153 Chain B: K.590 Ligands: PEG.4 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.590, B:K.590, A:R.73, A:K.153 PEG.4: 7 residues within 4Å: Chain A: R.78, E.114, M.138, I.155 Chain B: L.587, K.590 Ligands: PEG.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.78, A:E.114 Water bridges: A:K.139, A:K.153 PEG.22: 8 residues within 4Å: Chain B: Q.324, K.327, F.328, K.331, E.449, Y.540, E.544, Y.674 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.327, B:K.331, B:K.331, B:Y.540

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 2 residues within 4Å: Chain A: Y.144, Y.145 No protein-ligand interaction detected (PLIP) EDO.6: 3 residues within 4Å: Chain A: E.29 Chain B: H.53, P.286 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.52 EDO.23: 4 residues within 4Å: Chain B: S.564, K.618, F.622, I.700 No protein-ligand interaction detected (PLIP) EDO.24: 7 residues within 4Å: Chain B: N.546, I.547, S.550, E.636, N.639, V.640, S.643 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.550, B:S.643 EDO.25: 4 residues within 4Å: Chain B: N.393, L.396, E.397, Q.400 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.393, B:Q.400 EDO.26: 6 residues within 4Å: Chain A: M.133, G.134 Chain B: N.572, S.576, E.581, I.584 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.572, A:M.133 Water bridges: B:N.572 EDO.27: 4 residues within 4Å: Chain B: V.641, D.645, K.679, K.683 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.645, B:K.679, B:K.683 EDO.28: 6 residues within 4Å: Chain B: E.544, I.547, T.548, Y.674, L.678, F.722 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.544 EDO.29: 5 residues within 4Å: Chain B: N.688, V.691, I.692, T.726, L.727 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.727

9 x IOD: IODIDE ION(Non-functional Binders)

IOD.7: 3 residues within 4Å: Chain A: R.140 Chain B: R.410, Q.411 Ligand excluded by PLIP IOD.8: 3 residues within 4Å: Chain B: K.461, P.462, F.463 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain B: E.121, Y.276, R.281 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain B: T.109, P.111 Ligand excluded by PLIP IOD.11: 3 residues within 4Å: Chain B: S.422, L.423, Q.426 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain B: Q.284 Chain C: G.54 Ligand excluded by PLIP IOD.13: 1 residues within 4Å: Chain B: T.159 Ligand excluded by PLIP IOD.14: 2 residues within 4Å: Chain B: T.630, V.693 Ligand excluded by PLIP IOD.30: 1 residues within 4Å: Chain C: S.7 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grunwald, S. et al., Divergent architecture of the heterotrimeric NatC complex explains N-terminal acetylation of cognate substrates. Nat Commun (2020)

Release Date

2020-10-28

Peptides

N-alpha-acetyltransferase 30: A
N-alpha-acetyltransferase 35, NatC auxiliary subunit: B
N-alpha-acetyltransferase 38, NatC auxiliary subunit: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

N-alpha-acetyltransferase 30

N-alpha-acetyltransferase 35, NatC auxiliary subunit

N-alpha-acetyltransferase 38, NatC auxiliary subunit

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