SMTL ID : 5w5t.3 (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

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

SO4.1: 5 residues within 4Å: Chain A: R.28, Y.34, R.40, S.67, H.374 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.34, A:S.67, A:S.67 Water bridges: A:R.40, A:R.40 Salt bridges: A:R.28, A:R.40, A:H.374 SO4.2: 4 residues within 4Å: Chain A: S.329, N.345, S.346, R.363 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.329, A:S.329, A:S.346 Water bridges: A:R.363 Salt bridges: A:R.363 SO4.3: 4 residues within 4Å: Chain A: R.263, D.264, V.265, A.270 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.264, A:V.265 Water bridges: A:T.267 SO4.4: 3 residues within 4Å: Chain A: I.190, N.193, R.246 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.193 Salt bridges: A:R.246 SO4.5: 5 residues within 4Å: Chain A: L.156, E.157, F.247, A.248, P.260 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.157, A:E.157, A:A.248 Water bridges: A:F.247 SO4.9: 5 residues within 4Å: Chain B: S.329, N.345, S.346, R.363 Ligands: SO4.12 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.313, B:S.329, B:S.329, B:N.345, B:S.346, B:S.346, B:S.346 Salt bridges: B:R.363 SO4.10: 5 residues within 4Å: Chain B: R.28, Y.34, R.40, S.67, H.374 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Y.34, B:S.67 Water bridges: B:R.28, B:R.28, B:Y.34 Salt bridges: B:R.28, B:R.40, B:H.374 SO4.11: 5 residues within 4Å: Chain B: W.262, R.263, D.264, V.265, A.270 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.264, B:V.265 Water bridges: B:D.264, B:D.264, B:D.264, B:G.266 SO4.12: 3 residues within 4Å: Chain B: R.313, R.363 Ligands: SO4.9 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.363 Salt bridges: B:R.313, B:R.363 SO4.15: 5 residues within 4Å: Chain C: R.28, Y.34, R.40, S.67, H.374 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:Y.34, C:S.67 Water bridges: C:R.28, C:Y.34, C:R.40, C:H.374, C:H.374 Salt bridges: C:R.28, C:R.40, C:H.374 SO4.16: 6 residues within 4Å: Chain C: H.308, R.313, S.329, N.345, S.346, R.363 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:S.329, C:S.329, C:S.346, C:S.346, C:S.346 Water bridges: C:R.363 Salt bridges: C:H.308, C:R.313, C:R.363 SO4.17: 4 residues within 4Å: Chain C: R.263, D.264, V.265, A.270 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:D.264, C:V.265 Water bridges: C:R.263, C:R.263, C:D.264, C:G.266 SO4.21: 4 residues within 4Å: Chain D: S.329, N.345, S.346, R.363 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.329, D:N.345, D:S.346 Salt bridges: D:R.363 SO4.22: 5 residues within 4Å: Chain D: R.28, Y.34, R.40, S.67, H.374 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:Y.34, D:S.67, D:S.67 Water bridges: D:R.40, D:R.40, D:R.40, D:R.70 Salt bridges: D:R.28, D:R.40, D:H.374

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: R.80 Chain C: A.298, E.299, I.300 Chain D: A.298, I.300 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: A:R.80, A:R.80, C:E.299 Water bridges: D:I.300, C:A.298 GOL.7: 7 residues within 4Å: Chain A: T.105, G.202, Y.204, D.227, F.228, G.229, K.230 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.204, A:Y.204, A:D.227, A:F.228, A:G.229, A:K.230, A:K.230 Water bridges: A:S.200 GOL.13: 3 residues within 4Å: Chain B: R.20, T.398, E.399 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.20, B:E.399 Water bridges: B:S.400 GOL.14: 3 residues within 4Å: Chain B: I.190, N.193, R.246 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.193, B:R.246, B:R.246 GOL.18: 6 residues within 4Å: Chain A: A.298, I.300 Chain B: A.298, I.300 Chain C: R.80 Chain D: R.80 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 2 interactions with chain D Water bridges: A:A.298, A:A.298 Hydrogen bonds: C:R.80, D:R.80, D:R.80 GOL.19: 6 residues within 4Å: Chain C: T.105, Y.204, D.227, F.228, G.229, K.230 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.105, C:T.105, C:Y.204, C:G.229, C:K.230 Water bridges: C:T.105 GOL.23: 2 residues within 4Å: Chain D: K.22, R.396 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.396, D:R.396 Water bridges: D:K.22

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

9X7.8: 15 residues within 4Å: Chain A: K.38, T.301, P.303, A.304, V.322, S.323, G.324 Chain B: K.38, T.301, P.302, P.303, A.304, V.322, S.323, G.324 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:A.304, A:G.324, B:K.38, B:A.304 Salt bridges: A:K.38, B:K.38 Hydrophobic interactions: B:A.304 9X7.20: 15 residues within 4Å: Chain C: K.38, E.299, T.301, P.302, P.303, A.304, V.322, S.323, G.324 Chain D: K.38, P.302, P.303, V.322, S.323, G.324 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:K.38, D:G.324, C:A.304, C:G.324 Water bridges: D:T.301, C:K.38 Salt bridges: D:K.38, C:K.38 Hydrophobic interactions: C:T.301

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
O

B
P

C
G

D
H

Glucose-1-phosphate adenylyltransferase

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