SMTL ID : 5vbx.1

Crystal structure of holo-[acyl-carrier-protein] synthase (AcpS) from Escherichia coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-trimer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: K.86, P.87, V.109, T.110, L.111 Chain B: L.6, K.62 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.86, A:T.110 Water bridges: A:G.85, A:K.86 EDO.2: 4 residues within 4Å: Chain A: Q.45, P.46, V.47, R.48 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.47, A:R.48 Water bridges: A:R.48 EDO.6: 6 residues within 4Å: Chain B: K.86, P.87, V.109, T.110, L.111 Chain C: K.62 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:K.86, B:T.110, B:L.111, B:L.111, C:L.6 Water bridges: C:K.62 EDO.7: 6 residues within 4Å: Chain B: P.87, R.88, L.89, M.107, H.108, V.109 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:L.89, B:V.109 Water bridges: B:P.87, B:R.88, B:M.107, B:M.107 EDO.8: 4 residues within 4Å: Chain B: Q.45, P.46, V.47, R.48 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.45, B:V.47, B:R.48 EDO.10: 4 residues within 4Å: Chain C: Q.45, P.46, V.47, R.48 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.47, C:R.48 EDO.11: 7 residues within 4Å: Chain A: K.62 Chain C: G.85, K.86, P.87, V.109, T.110, L.111 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.85, C:T.110, C:L.111 EDO.12: 1 residues within 4Å: Chain C: R.69 No protein-ligand interaction detected (PLIP)

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

NA.3: 5 residues within 4Å: Chain A: E.12, Y.117 Chain C: E.114, R.115, H.116 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:H.116, A:E.12 NA.4: 6 residues within 4Å: Chain A: V.19, I.20, S.23, G.24, R.26, L.27 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.23, A:R.26, A:L.27 NA.5: 5 residues within 4Å: Chain A: E.114, R.115, H.116 Chain B: E.12, Y.117 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.12, B:Y.117, A:R.115, A:H.116 NA.9: 5 residues within 4Å: Chain B: E.114, R.115, H.116 Chain C: E.12, Y.117 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:E.114, B:R.115, B:H.116, C:Y.117 NA.13: 3 residues within 4Å: Chain C: R.88, L.89, M.107 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.89, C:L.89 NA.14: 6 residues within 4Å: Chain C: V.19, I.20, S.23, G.24, R.26, L.27 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.23, C:L.27 Water bridges: C:A.28 NA.15: 3 residues within 4Å: Chain C: F.80, N.81 Ligands: NA.17 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.81, C:N.81, C:N.81 NA.16: 4 residues within 4Å: Chain C: E.12, I.13, A.14, H.116 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:I.13, C:A.14, C:H.116 Water bridges: C:E.12 NA.17: 2 residues within 4Å: Chain C: R.53 Ligands: NA.15 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.53, C:R.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marcella, A.M. et al., Structure, High Affinity, and Negative Cooperativity of the Escherichia coli Holo-(Acyl Carrier Protein):Holo-(Acyl Carrier Protein) Synthase Complex. J. Mol. Biol. (2017)

Release Date

2017-11-01

Peptides

Holo-[acyl-carrier-protein] synthase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Holo-[acyl-carrier-protein] synthase

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