SMTL ID : 5w5t.4 (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

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

SO4.1: 5 residues within 4Å: Chain A: R.313, S.329, N.345, S.346, R.363 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.313, A:S.329, A:S.329, A:S.346, A:S.346, A:S.346 Water bridges: A:R.363 Salt bridges: A:R.363 SO4.2: 5 residues within 4Å: Chain A: R.28, Y.34, R.40, S.67, H.374 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.34, A:S.67 Water bridges: A:R.27, A:R.40 Salt bridges: A:R.28, A:R.40, A:H.374 SO4.3: 5 residues within 4Å: Chain A: R.263, D.264, V.265, G.266, A.270 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.264, A:V.265, A:G.266 Water bridges: A:W.262, A:R.263, A:T.267 SO4.4: 3 residues within 4Å: Chain A: D.269, T.398, E.399 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.399 Water bridges: A:T.398 SO4.9: 4 residues within 4Å: Chain B: S.329, N.345, S.346, R.363 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.329, B:N.345, B:S.346 Water bridges: B:N.345 Salt bridges: B:R.363 SO4.10: 4 residues within 4Å: Chain B: R.28, Y.34, R.40, S.67 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.34, B:S.67, B:S.67 Water bridges: B:R.40 Salt bridges: B:R.28, B:R.40 SO4.11: 2 residues within 4Å: Chain B: K.22, R.396 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.22 Salt bridges: B:K.22, B:R.396 SO4.16: 5 residues within 4Å: Chain C: R.28, Y.34, R.40, S.67, H.374 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Y.34, C:S.67, C:S.67 Water bridges: C:R.28, C:R.28 Salt bridges: C:R.28, C:R.40 SO4.17: 4 residues within 4Å: Chain C: S.329, N.345, S.346, R.363 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.329, C:S.329, C:S.346 Water bridges: C:N.345 Salt bridges: C:R.363 SO4.18: 5 residues within 4Å: Chain C: R.263, D.264, V.265, G.266, A.270 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.264, C:V.265, C:G.266 Water bridges: C:A.270 SO4.24: 4 residues within 4Å: Chain D: S.329, N.345, S.346, R.363 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.329, D:S.329, D:S.346, D:S.346 Water bridges: D:R.313 Salt bridges: D:R.363 SO4.25: 6 residues within 4Å: Chain D: R.28, Y.34, R.40, S.67, R.70, H.374 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:Y.34, D:S.67, D:R.70 Water bridges: D:R.28, D:R.28, D:Y.34, D:R.40 Salt bridges: D:R.28, D:R.40, D:H.374 SO4.26: 5 residues within 4Å: Chain D: R.263, D.264, V.265, G.266, A.270 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.264, D:V.265, D:G.266 Water bridges: D:D.264

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: D.280, V.281, V.282 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.280, A:V.281, A:V.282 Water bridges: A:D.280 GOL.6: 5 residues within 4Å: Chain A: T.105, Y.204, D.227, F.228, G.229 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.105, A:Y.204, A:F.228, A:G.229 Water bridges: A:Y.204, A:K.230 GOL.7: 4 residues within 4Å: Chain A: R.17, G.18, S.19, R.20 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.17, A:G.18, A:S.19, A:R.20, A:R.20 Water bridges: A:D.130 GOL.12: 4 residues within 4Å: Chain B: R.17, G.18, S.19, R.20 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.17, B:G.18, B:S.19, B:S.19, B:R.20, B:R.20, B:R.20 GOL.13: 6 residues within 4Å: Chain B: T.105, G.202, Y.204, D.227, F.228, G.229 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.204, B:D.227, B:D.227, B:G.229 GOL.14: 8 residues within 4Å: Chain A: R.80 Chain B: R.80, E.82 Chain C: W.295, A.298, E.299, I.300 Chain D: A.298 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: C:I.300, B:E.82, A:R.80 Water bridges: C:A.298 GOL.15: 5 residues within 4Å: Chain A: K.305, I.327 Chain B: P.283, D.286, Y.288 2 PLIP interactions: 2 interactions with chain B Water bridges: B:L.285, B:I.287 GOL.19: 6 residues within 4Å: Chain A: E.85 Chain C: L.50, I.54, R.55, F.78, E.85 4 PLIP interactions: 4 interactions with chain C Water bridges: C:L.50, C:F.78, C:R.83, C:E.85 GOL.20: 5 residues within 4Å: Chain C: T.105, Y.204, D.227, F.228, G.229 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.204, C:D.227, C:D.227, C:F.228, C:G.229 GOL.21: 8 residues within 4Å: Chain C: A.14, G.15, A.60, T.61, Q.62, Y.102, G.104, T.105 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.15, C:A.60, C:Q.62 Water bridges: C:G.16 GOL.22: 4 residues within 4Å: Chain C: D.269, T.398, E.399, S.400 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.399, C:S.400 Water bridges: C:I.268 GOL.27: 5 residues within 4Å: Chain D: T.105, Y.204, D.227, F.228, G.229 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.105, D:Y.204, D:D.227, D:F.228, D:G.229 GOL.28: 2 residues within 4Å: Chain D: R.313, R.363 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.313, D:R.313, D:R.363, D:R.363

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

9X7.8: 14 residues within 4Å: Chain A: K.38, P.302, P.303, A.304, V.322, S.323, G.324 Chain B: K.38, T.301, P.302, P.303, V.322, S.323, G.324 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:A.304 Hydrogen bonds: A:A.304, A:G.324, B:K.38 Salt bridges: A:K.38, B:K.38 9X7.23: 16 residues within 4Å: Chain C: K.38, T.301, 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 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:A.304, C:G.324, D:K.38, D:A.304 Salt bridges: C:K.38, D:K.38 Hydrophobic interactions: D: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
I

B
J

C
M

D
N

Glucose-1-phosphate adenylyltransferase

Related Entries With Identical Sequence