SMTL ID : 1yp4.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 8 residues within 4Å: Chain A: R.41, P.47, R.53, S.80, R.83, D.370, K.404, K.441 Ligand excluded by PLIP SO4.2: 4 residues within 4Å: Chain A: K.69, E.133, H.134, T.135 Ligand excluded by PLIP SO4.3: 5 residues within 4Å: Chain A: R.53, R.83, H.84, Q.314, R.316 Ligand excluded by PLIP SO4.4: 8 residues within 4Å: Chain A: G.28, G.29, A.30, G.31, T.32, R.33, K.43 Ligands: ADP.5 Ligand excluded by PLIP SO4.6: 7 residues within 4Å: Chain B: R.41, P.47, R.53, S.80, D.370, K.404, K.441 Ligand excluded by PLIP SO4.7: 5 residues within 4Å: Chain B: K.69, E.99, H.134, T.135 Chain C: R.87 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain B: R.53, H.84, Q.314, R.316 Ligand excluded by PLIP SO4.9: 7 residues within 4Å: Chain B: G.29, A.30, G.31, T.32, R.33, K.43 Ligands: ADQ.10 Ligand excluded by PLIP SO4.11: 7 residues within 4Å: Chain C: R.41, P.47, R.53, S.80, D.370, K.404, K.441 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain B: R.83 Chain C: K.69, H.134, T.135 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain C: R.53, H.84, Q.314, R.316 Ligand excluded by PLIP SO4.14: 7 residues within 4Å: Chain C: G.28, G.29, A.30, G.31, T.32, K.43 Ligands: ADP.15 Ligand excluded by PLIP SO4.16: 7 residues within 4Å: Chain D: R.41, P.47, R.53, S.80, D.370, K.404, K.441 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain D: K.69, H.134, T.135 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain D: R.53, H.84, Q.314, R.316 Ligand excluded by PLIP SO4.19: 5 residues within 4Å: Chain D: G.29, A.30, G.31, T.32, R.33 Ligand excluded by PLIP

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.5: 16 residues within 4Å: Chain A: L.26, G.27, G.28, G.29, K.43, L.73, Q.118, T.120, A.123, A.143, G.144, D.145, D.253, G.255, S.256 Ligands: SO4.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.28, A:Q.75, A:Q.118, A:T.120, A:G.144, A:D.145, A:D.145, A:G.255, A:S.256, A:S.256 ADP.15: 17 residues within 4Å: Chain C: L.26, G.27, G.28, G.29, K.43, L.73, Q.118, T.120, A.123, A.143, G.144, D.145, D.253, F.254, G.255, S.256 Ligands: SO4.14 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:G.28, C:K.43, C:Q.75, C:Q.118, C:G.144, C:D.145, C:F.254, C:G.255, C:S.256 Water bridges: C:Q.118, C:T.120

1 x ADQ: ADENOSINE-5'-DIPHOSPHATE-GLUCOSE(Non-covalent)

ADQ.10: 25 residues within 4Å: Chain B: L.26, G.27, G.28, G.29, R.33, K.43, L.73, Q.118, G.119, T.120, A.123, A.143, D.145, H.146, F.181, G.182, E.197, K.198, S.229, M.230, G.231, G.255, W.278, D.280 Ligands: SO4.9 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:R.33, B:K.43, B:Q.118, B:T.120, B:D.145, B:H.146, B:G.182, B:G.182, B:E.197, B:S.229, B:S.229, B:D.253, B:D.253, B:G.255, B:D.280 Water bridges: B:H.146, B:Y.233, B:Y.233, B:D.280 Salt bridges: B:R.33, B:K.198, B:K.198

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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