SMTL ID : 1yp3.1

Crystal structure of potato tuber ADP-glucose pyrophosphorylase in complex with ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: R.41, P.47, R.53, S.80, D.370, K.404, K.441 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: 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 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:T.135, A:T.135 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.314 Water bridges: A:R.352, A:K.404 Salt bridges: A:R.53, A:H.84, A:R.316 SO4.4: 6 residues within 4Å: Chain A: G.29, G.31, T.32, R.33, K.43 Ligands: ATP.5 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.29, A:G.31, A:T.32, A:T.32, A:T.32, A:R.33 Salt bridges: A:R.33, A:K.43 SO4.6: 7 residues within 4Å: Chain B: R.41, P.47, R.53, S.80, D.370, K.404, K.441 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.80, B:D.370 Water bridges: B:K.441 Salt bridges: B:R.41, B:R.53, B:K.404, B:K.441 SO4.7: 3 residues within 4Å: Chain B: K.69, H.134, T.135 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.135 Salt bridges: B:K.69, B:H.134 SO4.8: 4 residues within 4Å: Chain B: R.53, H.84, Q.314, R.316 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.314, B:Q.314 Salt bridges: B:R.53, B:H.84, B:R.316, B:K.404 SO4.9: 7 residues within 4Å: Chain C: R.41, P.47, R.53, S.80, D.370, K.404, K.441 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.80 Salt bridges: C:R.41, C:R.53, C:K.404, C:K.441 SO4.10: 5 residues within 4Å: Chain B: R.83 Chain C: K.69, E.133, H.134, T.135 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:T.135 Water bridges: C:H.134 Salt bridges: C:K.69, C:H.134, B:R.83 SO4.11: 4 residues within 4Å: Chain C: R.53, H.84, Q.314, R.316 5 PLIP interactions: 5 interactions with chain C Water bridges: C:R.316, C:R.316 Salt bridges: C:R.53, C:H.84, C:R.316 SO4.12: 8 residues within 4Å: Chain C: G.28, G.29, A.30, G.31, T.32, R.33, K.43 Ligands: ATP.13 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.29, C:A.30, C:G.31, C:T.32, C:R.33 Salt bridges: C:K.43 SO4.14: 7 residues within 4Å: Chain D: R.41, P.47, R.53, S.80, D.370, K.404, K.441 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.80, D:D.370 Salt bridges: D:R.41, D:R.53, D:K.404, D:K.441 SO4.15: 5 residues within 4Å: Chain D: R.53, H.84, Q.314, R.316, K.404 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:Q.314 Water bridges: D:R.352, D:R.352, D:R.352, D:R.352 Salt bridges: D:R.53, D:H.84, D:R.316, D:K.404

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.5: 19 residues within 4Å: Chain A: L.26, G.28, G.29, K.43, L.73, Q.75, Q.118, G.119, T.120, A.123, A.143, G.144, D.145, Y.233, D.253, F.254, G.255, S.256 Ligands: SO4.4 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.28, A:K.43, A:Q.118, A:T.120, A:T.120, A:D.145, A:D.253, A:F.254, A:G.255, A:S.256 Water bridges: A:Q.118, A:G.144 Salt bridges: A:R.33 ATP.13: 20 residues within 4Å: Chain C: L.26, G.27, G.28, G.29, K.43, L.73, Q.118, G.119, T.120, A.123, A.143, G.144, D.145, H.146, G.231, D.253, F.254, G.255, S.256 Ligands: SO4.12 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:G.28, C:K.43, C:Q.75, C:Q.118, C:T.120, C:T.120, C:G.144, C:D.145, C:D.145, C:G.255, C:S.256 Water bridges: C:T.120, C:D.253 Salt bridges: C:H.146

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

Related Entries With Identical Sequence