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

Agrobacterium tumefaciens ADP-Glucose Pyrophosphorylase bound to activator ethyl pyruvate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: R.313, S.329, N.345, S.346, R.363 Ligands: SO4.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.313, A:S.329, A:S.329, A:S.346, A:S.346, A:S.346 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.28, A:Y.34 Salt bridges: A:R.28, A:R.40, A:H.374 SO4.3: 3 residues within 4Å: Chain A: R.313, R.363 Ligands: SO4.1 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.313 Salt bridges: A:R.313, A:R.363 SO4.6: 4 residues within 4Å: Chain B: S.329, N.345, S.346, R.363 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.329, B:S.329, B:S.346, B:S.346 Water bridges: B:N.345, B:N.345 Salt bridges: B:R.363 SO4.7: 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, B:S.67 Water bridges: B:R.28, B:H.66, B:H.374 Salt bridges: B:R.28, B:R.40 SO4.8: 4 residues within 4Å: Chain B: 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:R.263, B:D.264, B:T.267, B:A.270 SO4.9: 2 residues within 4Å: Chain B: T.398, E.399 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.399 Water bridges: B:I.268 SO4.13: 6 residues within 4Å: Chain C: R.28, Y.34, R.40, S.67, R.70, H.374 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:Y.34, C:S.67, C:R.70 Water bridges: C:R.28, C:R.28, C:R.28, C:H.374 Salt bridges: C:R.28, C:R.40, C:H.374 SO4.14: 4 residues within 4Å: Chain C: S.329, N.345, S.346, R.363 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.329, C:S.329, C:S.346 Salt bridges: C:R.363 SO4.15: 4 residues within 4Å: Chain C: R.263, D.264, V.265, A.270 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.264, C:V.265 Water bridges: C:W.262, C:T.267 SO4.19: 5 residues within 4Å: Chain D: S.329, N.345, S.346, R.363 Ligands: SO4.22 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.329, D:N.345, D:S.346 Water bridges: D:N.345 Salt bridges: D:R.363 SO4.20: 5 residues within 4Å: Chain D: R.28, Y.34, R.40, S.67, H.374 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Y.34, D:S.67, D:S.67 Salt bridges: D:R.28, D:R.40, D:H.374 SO4.21: 5 residues within 4Å: Chain D: W.262, R.263, D.264, V.265, A.270 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.264, D:V.265 Water bridges: D:G.266, D:T.267 SO4.22: 3 residues within 4Å: Chain D: R.313, R.363 Ligands: SO4.19 3 PLIP interactions: 3 interactions with chain D Water bridges: D:R.363 Salt bridges: D:R.313, D:R.363

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: T.105, Y.204, D.227, F.228, G.229 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.105, A:Y.204, A:G.229 Water bridges: A:Y.204, A:K.230 GOL.5: 7 residues within 4Å: Chain A: P.283, L.285, D.286, I.287, Y.288 Chain B: K.305, I.327 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.285, A:D.286, A:I.287 Water bridges: A:V.281 GOL.10: 5 residues within 4Å: Chain B: T.105, Y.204, D.227, F.228, G.229 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.204, B:D.227, B:F.228, B:G.229 Water bridges: B:G.202, B:K.230 GOL.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.16: 3 residues within 4Å: Chain C: D.280, V.281, V.282 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:V.281, C:V.282 Water bridges: C:T.279, C:D.280 GOL.17: 5 residues within 4Å: Chain C: T.105, G.202, Y.204, F.228, G.229 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.105, C:D.227, C:G.229 Water bridges: C:Y.204 GOL.23: 3 residues within 4Å: Chain D: I.190, N.193, R.246 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.193, D:R.246, D:R.246 Water bridges: D:E.157, D:E.157, D:D.175, D:N.193

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

9X7.12: 14 residues within 4Å: Chain A: K.38, P.302, P.303, A.304, S.323, G.324 Chain B: K.38, E.299, T.301, P.302, P.303, V.322, S.323, G.324 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.324, B:K.38, B:G.324 Salt bridges: A:K.38, B:K.38 9X7.18: 15 residues within 4Å: Chain C: K.38, T.301, 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 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:A.304 Hydrogen bonds: C:A.304, C:G.324, D:K.38, D:A.304 Water bridges: C:K.38 Salt bridges: C:K.38, D:K.38

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
K

B
L

C
Z

D
T

Glucose-1-phosphate adenylyltransferase

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