SMTL ID : 5w5t.2 (4 other biounits)

Agrobacterium tumefaciens ADP-Glucose Pyrophosphorylase bound to activator ethyl pyruvate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-tetramer

Ligands

19 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: S.329, N.345, S.346, R.363 Ligand excluded by PLIP SO4.2: 5 residues within 4Å: Chain A: R.28, Y.34, R.40, S.67, H.374 Ligand excluded by PLIP SO4.3: 5 residues within 4Å: Chain A: W.262, R.263, D.264, V.265, A.270 Ligand excluded by PLIP SO4.4: 6 residues within 4Å: Chain A: L.156, E.157, F.247, A.248, P.260 Ligands: GOL.11 Ligand excluded by PLIP SO4.5: 2 residues within 4Å: Chain A: T.398, E.399 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: T.105, Y.204, F.228, G.229 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain A: I.190, N.193, R.246 Ligand excluded by PLIP SO4.8: 2 residues within 4Å: Chain A: K.22, R.396 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain B: S.329, N.345, S.346, R.363 Ligand excluded by PLIP SO4.13: 6 residues within 4Å: Chain B: R.28, Y.34, R.40, S.67, R.70, H.374 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain B: R.263, D.264, V.265, A.270 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain B: D.269, T.398, E.399 Ligand excluded by PLIP SO4.16: 1 residues within 4Å: Chain B: R.396 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain B: R.313, R.363 Ligand excluded by PLIP SO4.23: 5 residues within 4Å: Chain C: R.28, Y.34, R.40, S.67, H.374 Ligand excluded by PLIP SO4.24: 5 residues within 4Å: Chain C: R.313, S.329, N.345, S.346, R.363 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain C: R.263, D.264, V.265, A.270 Ligand excluded by PLIP SO4.27: 4 residues within 4Å: Chain D: R.28, Y.34, R.40, S.67 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain D: S.329, N.345, S.346, R.363 Ligand excluded by PLIP

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 2 residues within 4Å: Chain A: R.313, R.363 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.313, A:R.363, A:R.363 Water bridges: A:H.308 GOL.10: 6 residues within 4Å: Chain A: W.295, A.298 Chain B: A.298, I.300 Chain C: R.80 Chain D: R.80 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: A:E.299 Water bridges: A:A.298, D:R.80, B:A.298 GOL.11: 4 residues within 4Å: Chain A: E.259, P.260, W.262 Ligands: SO4.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.259 Water bridges: A:W.262, A:R.263 GOL.18: 3 residues within 4Å: Chain B: D.280, V.281, V.282 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.281, B:V.282, B:V.282 Water bridges: B:D.280 GOL.19: 4 residues within 4Å: Chain D: L.50, R.55, F.78, E.85 4 PLIP interactions: 4 interactions with chain D Water bridges: D:F.78, D:R.83, D:E.85, D:E.85 GOL.20: 4 residues within 4Å: Chain B: E.157, I.190, N.193, R.246 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.193, B:R.246, B:R.246 Water bridges: B:E.157, B:E.173, B:D.175 GOL.21: 4 residues within 4Å: Chain B: L.156, E.157, A.248, P.260 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.157 Water bridges: B:A.248, B:A.248, B:E.259, B:P.260 GOL.26: 6 residues within 4Å: Chain C: T.105, G.202, Y.204, D.227, F.228, G.229 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.105, C:T.105, C:F.228, C:G.229 Water bridges: C:K.230, C:K.230

2 x 9X7: ethyl 2-oxopropanoate(Non-covalent)

9X7.22: 15 residues within 4Å: Chain A: K.38, E.299, T.301, P.302, P.303, V.322, S.323, G.324 Chain B: K.38, P.302, P.303, A.304, V.322, S.323, G.324 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:A.304 Hydrogen bonds: B:A.304, B:G.324, A:K.38, A:G.324 Salt bridges: B:K.38, A:K.38 9X7.29: 15 residues within 4Å: Chain C: K.38, P.302, P.303, A.304, V.322, S.323, G.324 Chain D: K.38, T.301, P.302, P.303, A.304, V.322, S.323, G.324 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:A.304, D:G.324, C:K.38 Salt bridges: D:K.38, C:K.38 Hydrophobic interactions: C:A.304

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hill, B.L. et al., Structural analysis reveals a pyruvate-binding activator site in theAgrobacterium tumefaciensADP-glucose pyrophosphorylase. J. Biol. Chem. (2019)

Release Date

2018-11-14

Peptides

Glucose-1-phosphate adenylyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Q

B
R

C
E

D
F

Glucose-1-phosphate adenylyltransferase

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