SMTL ID : 2fad.3 (2 other biounits)

Crystal structure of E. coli heptanoyl-ACP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

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

NA.1: 3 residues within 4Å: Chain A: S.1 Chain B: D.51 Chain D: A.77 5 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: A:S.1, D:A.77 Water bridges: B:D.51, B:D.51, B:D.51 NA.12: 3 residues within 4Å: Chain B: A.77 Chain C: S.1 Chain D: D.51 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:S.1, D:D.51 Water bridges: D:D.51, D:D.51, D:D.51

16 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.2: 2 residues within 4Å: Chain A: E.5 Chain B: E.48 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:E.48, A:E.5, A:E.5, H2O.5 ZN.3: 1 residues within 4Å: Chain A: E.21 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.21, H2O.2, H2O.4 ZN.4: 1 residues within 4Å: Chain A: D.35 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.35, H2O.3, H2O.5 ZN.5: 1 residues within 4Å: Chain A: D.56 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.56, H2O.1, H2O.1 ZN.6: 2 residues within 4Å: Chain A: E.48 Chain B: E.5 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:E.5, A:E.48, H2O.6 ZN.7: 3 residues within 4Å: Chain A: A.77 Chain C: A.77 Ligands: ZN.18 No protein-ligand interaction detected (PLIP) ZN.8: 2 residues within 4Å: Chain A: E.57, E.60 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.57, A:E.57, A:E.60, A:E.60 ZN.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.13: 2 residues within 4Å: Chain C: E.5 Chain D: E.48 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: C:E.5, C:E.5, D:E.48, H2O.13 ZN.14: 1 residues within 4Å: Chain C: E.21 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.21, H2O.10, H2O.12 ZN.15: 1 residues within 4Å: Chain C: D.35 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.35, H2O.10, H2O.12 ZN.16: 1 residues within 4Å: Chain C: D.56 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.56, H2O.9, H2O.9 ZN.17: 2 residues within 4Å: Chain C: E.48 Chain D: E.5 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: C:E.48, D:E.5, H2O.13 ZN.18: 3 residues within 4Å: Chain A: A.77 Chain C: A.77 Ligands: ZN.7 No protein-ligand interaction detected (PLIP) ZN.19: 2 residues within 4Å: Chain C: E.57, E.60 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.57, C:E.57, C:E.60, C:E.60 ZN.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

4 x PM5: S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) HEPTANETHIOATE(Covalent)

PM5.9: 16 residues within 4Å: Chain A: F.28, V.29, D.35, S.36, T.39, L.42, V.43, L.46, E.47, T.52, I.54, A.59, E.60, I.62, Y.71, I.72 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.46, A:L.46, A:T.52, A:I.54, A:Y.71, A:Y.71, A:I.72 Hydrogen bonds: A:D.35, A:A.59 Water bridges: A:S.36 PM5.11: 10 residues within 4Å: Chain B: F.28, V.29, S.36, T.39, L.46, I.54, A.59, E.60, I.62, A.68 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.28, B:V.29, B:V.29, B:L.46, B:I.54, B:E.60, B:I.62, B:A.68 PM5.20: 16 residues within 4Å: Chain C: F.28, V.29, D.35, S.36, T.39, L.42, V.43, L.46, E.47, T.52, I.54, A.59, E.60, I.62, Y.71, I.72 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:L.46, C:L.46, C:T.52, C:I.54, C:Y.71, C:Y.71, C:I.72 Hydrogen bonds: C:D.35, C:A.59 Water bridges: C:S.36 PM5.22: 10 residues within 4Å: Chain D: F.28, V.29, S.36, T.39, L.46, I.54, A.59, E.60, I.62, A.68 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.28, D:V.29, D:V.29, D:L.46, D:I.54, D:E.60, D:I.62, D:A.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roujeinikova, A. et al., Structural Studies of Fatty Acyl-(Acyl Carrier Protein) Thioesters Reveal a Hydrophobic Binding Cavity that Can Expand to Fit Longer Substrates. J.Mol.Biol. (2007)

Release Date

2006-09-26

Peptides

Acyl carrier protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Acyl carrier protein

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