SMTL ID : 1yp2.1

Crystal structure of potato tuber ADP-glucose pyrophosphorylase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: R.41, P.47, R.53, D.370, K.404, K.441 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.370 Water bridges: A:R.53, A:S.80, A:S.80 Salt bridges: A:R.41, A:R.53, A:K.404, A:K.441 SO4.2: 5 residues within 4Å: Chain A: K.69, E.133, H.134, T.135 Chain D: R.83 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:T.135, A:T.135, A:T.135 Water bridges: A:K.69, A:H.134, D:R.83 Salt bridges: A:K.69, A:H.134, D:R.83 SO4.3: 4 residues within 4Å: Chain A: R.53, H.84, Q.314, R.316 9 PLIP interactions: 9 interactions with chain A Water bridges: A:S.80, A:R.83, A:R.83, A:R.352, A:K.404, A:K.404 Salt bridges: A:R.53, A:H.84, A:R.316 SO4.5: 7 residues within 4Å: Chain B: R.41, P.47, R.53, S.80, D.370, K.404, K.441 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.80, B:D.370 Water bridges: B:R.53, B:R.53 Salt bridges: B:R.41, B:R.53, B:K.404, B:K.441 SO4.6: 5 residues within 4Å: Chain B: K.69, E.133, H.134, T.135 Chain C: R.83 10 PLIP interactions: 2 interactions with chain C, 8 interactions with chain B Water bridges: C:R.87, B:K.69, B:K.69, B:K.69, B:H.134 Salt bridges: C:R.83, B:K.69, B:H.134 Hydrogen bonds: B:T.135, B:T.135 SO4.7: 4 residues within 4Å: Chain B: R.53, H.84, Q.314, R.316 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Q.314 Water bridges: B:R.53, B:R.316, B:R.352, B:R.352, B:R.352, B:D.370 Salt bridges: B:R.53, B:H.84, B:R.316 SO4.9: 7 residues within 4Å: Chain C: R.41, P.47, R.53, S.80, D.370, K.404, K.441 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:S.80, C:S.80 Water bridges: C:R.53, C:R.53 Salt bridges: C:R.41, C:R.53, C:K.404, C:K.441 SO4.10: 4 residues within 4Å: Chain B: R.83 Chain C: K.69, H.134, T.135 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain C Water bridges: B:R.83, C:K.69, C:K.69 Salt bridges: B:R.83, C:K.69, C:H.134 Hydrogen bonds: C:T.135, C:T.135 SO4.11: 4 residues within 4Å: Chain C: R.53, H.84, Q.314, R.316 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:Q.314 Water bridges: C:S.80, C:R.83, C:R.352, C:R.352, C:D.370, C:K.404 Salt bridges: C:R.53, C:H.84, C:R.316 SO4.13: 7 residues within 4Å: Chain D: R.41, P.47, R.53, S.80, D.370, K.404, K.441 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:S.80 Water bridges: D:R.53, D:R.53, D:R.53 Salt bridges: D:R.41, D:R.53, D:K.404, D:K.441 SO4.14: 4 residues within 4Å: Chain A: R.83 Chain D: K.69, H.134, T.135 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:T.135 Salt bridges: D:K.69, D:H.134, A:R.83 SO4.15: 4 residues within 4Å: Chain D: R.53, H.84, Q.314, R.316 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:Q.314 Water bridges: D:R.83, D:R.83, D:R.316, D:R.352, D:R.352, D:D.370, D:D.370, D:K.404, D:K.404 Salt bridges: D:R.53, D:H.84, D:R.316

4 x PMB: PARA-MERCURY-BENZENESULFONIC ACID(Non-covalent)(Covalent)

PMB.4: 9 residues within 4Å: Chain A: K.322, L.324, V.338, I.339, K.340, C.354, I.355 Chain B: K.297, P.298 8 PLIP interactions: 7 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:K.340 Water bridges: A:K.340 Salt bridges: A:K.322, A:K.340 pi-Cation interactions: A:K.340 Metal complexes: A:V.338, A:C.354, H2O.10 PMB.8: 10 residues within 4Å: Chain A: K.297, P.298 Chain B: K.322, L.324, V.338, I.339, K.340, C.354, I.355, R.378 8 PLIP interactions: 7 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:V.338, B:K.340, B:K.340 Salt bridges: B:K.322, B:K.340 pi-Cation interactions: B:K.340 Metal complexes: B:C.354, H2O.19 PMB.12: 10 residues within 4Å: Chain C: K.322, L.324, V.338, I.339, K.340, C.354, I.355, R.378 Chain D: K.297, P.298 7 PLIP interactions: 6 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: C:V.338, C:K.340, C:K.340 Salt bridges: C:K.322, C:K.340 Metal complexes: C:C.354, H2O.31 PMB.16: 10 residues within 4Å: Chain C: K.297, P.298 Chain D: K.322, L.324, V.338, I.339, K.340, C.354, I.355, R.378 6 PLIP interactions: 5 interactions with chain D, 1 Ligand-Water interactions Hydrophobic interactions: D:V.338, D:K.340 Salt bridges: D:K.322 pi-Cation interactions: D:K.340 Metal complexes: D:C.354, H2O.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jin, X. et al., Crystal structure of potato tuber ADP-glucose pyrophosphorylase. Embo J. (2005)

Release Date

2005-03-15

Peptides

Glucose-1-phosphate adenylyltransferase small subunit: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Glucose-1-phosphate adenylyltransferase small subunit

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