SMTL ID : 4xz3.1

Ca. Korarchaeum cryptofilum dinucleotide forming Acetyl-coenzyme A synthetase 1 (Se-Met derivative) in complex with coenzyme A and Mg-AMPPCP, phosphohistidine segment pointing towards nucleotide binding site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-oligomer

Ligands

2 x COA: COENZYME A(Non-covalent)

COA.1: 24 residues within 4Å: Chain A: V.16, G.17, S.19, K.24, I.25, I.45, N.46, P.47, P.59, S.74, V.75, P.76, K.79, V.83, I.98, T.99, S.100, N.129, I.130, F.131, F.144, G.161, A.162 Chain C: M.355 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.99 Hydrogen bonds: A:I.45, A:N.46, A:N.46, A:I.98, A:S.100 Salt bridges: A:K.24, A:K.24 COA.9: 26 residues within 4Å: Chain C: V.16, G.17, A.18, S.19, K.20, K.24, I.25, I.45, N.46, P.47, P.59, S.74, V.75, P.76, K.79, V.83, I.98, T.99, S.100, N.129, I.130, F.131, F.144, G.161, I.165, S.183 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:I.25, C:T.99 Hydrogen bonds: C:S.19, C:S.19, C:I.45, C:N.46, C:I.98, C:S.100 Salt bridges: C:K.24, C:K.24, C:K.24

4 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.2: 17 residues within 4Å: Chain A: G.307, G.308, G.309, F.343, A.344, S.345, D.351, T.353 Chain C: E.104, V.105, N.129, S.160, G.161, A.162, L.163, E.213 Ligands: MG.3 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:N.129, C:S.160, C:G.161, C:A.162, A:G.308, A:G.309, A:F.343 ACP.4: 18 residues within 4Å: Chain B: T.35, V.58, K.60, K.69, S.70, V.75, V.77, Q.111, E.112, F.113, A.114, V.141, P.212, V.223, D.224, R.226 Chain D: R.178 Ligands: MG.5 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.111, B:A.114, B:R.226 Water bridges: B:K.60, B:K.60, A:H.254 Salt bridges: B:K.60 ACP.6: 17 residues within 4Å: Chain A: E.104, V.105, N.129, S.160, G.161, A.162, L.163, E.213 Chain C: G.307, G.308, G.309, F.343, A.344, S.345, D.351, T.353 Ligands: MG.7 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:N.129, A:S.160, A:G.161, A:A.162, C:G.308, C:G.309, C:F.343, C:F.343 ACP.10: 15 residues within 4Å: Chain B: R.178 Chain D: V.58, K.69, S.70, V.75, Q.111, E.112, F.113, A.114, E.119, P.212, V.223, D.224, R.226 Ligands: MG.11 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain D Hydrogen bonds: B:R.178, D:S.70, D:Q.111, D:E.112, D:A.114, D:D.224, D:R.226

5 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: T.353, G.354 Ligands: ACP.2 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain B: K.60, P.212, D.224 Ligands: ACP.4 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.224, H2O.2 MG.7: 6 residues within 4Å: Chain C: G.307, G.308, D.351, T.353, G.354 Ligands: ACP.6 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain C: S.11, A.12, D.66 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.66 MG.11: 4 residues within 4Å: Chain D: N.211, P.212, D.224 Ligands: ACP.10 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.224

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weie, R.H. et al., Structure of NDP-forming Acetyl-CoA synthetase ACD1 reveals a large rearrangement for phosphoryl transfer. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-01-27

Peptides

Acyl-CoA synthetase (NDP forming): AC
Uncharacterized protein: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Acyl-CoA synthetase (NDP forming)

Uncharacterized protein

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