SMTL ID : 4b9y.1

Crystal Structure of Apo Agd31B, alpha-transglucosylase in Glycoside Hydrolase Family 31

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: P.322, T.323, P.324, L.325, D.326 Ligand excluded by PLIP SO4.2: 3 residues within 4Å: Chain A: R.797 Chain B: D.553, E.554 Ligand excluded by PLIP SO4.3: 2 residues within 4Å: Chain A: R.58, R.231 Ligand excluded by PLIP SO4.4: 4 residues within 4Å: Chain A: T.732, D.733, N.734, Q.735 Ligand excluded by PLIP SO4.5: 4 residues within 4Å: Chain A: G.239, N.240, S.244, N.248 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: T.97, E.98, N.99, H.100 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain A: T.648, D.649, G.650, A.651 Ligand excluded by PLIP SO4.8: 1 residues within 4Å: Chain A: R.274 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain A: S.63, E.64, Q.251 Ligand excluded by PLIP SO4.10: 2 residues within 4Å: Chain A: E.809, A.810 Ligand excluded by PLIP SO4.19: 5 residues within 4Å: Chain B: P.322, T.323, P.324, L.325, D.326 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain A: D.553, E.554 Chain B: R.797 Ligand excluded by PLIP SO4.21: 2 residues within 4Å: Chain B: R.58, R.231 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain B: T.732, D.733, N.734, Q.735 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain B: G.239, N.240, S.244, N.248 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain B: T.97, E.98, N.99, H.100 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain B: T.648, D.649, G.650, A.651 Ligand excluded by PLIP SO4.26: 1 residues within 4Å: Chain B: R.274 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain B: S.63, E.64, Q.251 Ligand excluded by PLIP SO4.28: 2 residues within 4Å: Chain B: E.809, A.810 Ligand excluded by PLIP

2 x OXL: OXALATE ION(Non-covalent)

OXL.11: 4 residues within 4Å: Chain A: H.731, S.764, R.798, K.817 11 PLIP interactions: 11 interactions with chain A Water bridges: A:H.731, A:H.731, A:D.765, A:D.765, A:Y.767, A:R.798, A:K.817 Salt bridges: A:H.731, A:R.798, A:K.817, A:K.817 OXL.29: 4 residues within 4Å: Chain B: H.731, S.764, R.798, K.817 11 PLIP interactions: 11 interactions with chain B Water bridges: B:H.731, B:H.731, B:D.765, B:D.765, B:Y.767, B:R.798, B:K.817 Salt bridges: B:H.731, B:R.798, B:K.817, B:K.817

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.12: 6 residues within 4Å: Chain A: Q.77, L.78, S.229, G.230, R.231, T.432 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.78, A:G.230 EDO.13: 4 residues within 4Å: Chain A: D.683, Y.684, R.685 Ligands: EDO.31 No protein-ligand interaction detected (PLIP) EDO.14: 3 residues within 4Å: Chain A: R.561, P.562, K.565 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.565 Water bridges: A:P.562 EDO.15: 4 residues within 4Å: Chain A: R.753, G.807, R.808, E.809 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.753, A:R.808, A:R.808 EDO.17: 4 residues within 4Å: Chain A: H.178, H.184, S.185, G.186 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.184, A:G.186, A:Q.187 EDO.18: 2 residues within 4Å: Chain A: T.743, G.744 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.744 EDO.30: 6 residues within 4Å: Chain B: Q.77, L.78, S.229, G.230, R.231, T.432 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.78, B:G.230 EDO.31: 4 residues within 4Å: Chain B: D.683, Y.684, R.685 Ligands: EDO.13 No protein-ligand interaction detected (PLIP) EDO.32: 3 residues within 4Å: Chain B: R.561, P.562, K.565 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.565 Water bridges: B:P.562 EDO.33: 4 residues within 4Å: Chain B: R.753, G.807, R.808, E.809 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.753, B:R.808, B:R.808 EDO.35: 4 residues within 4Å: Chain B: H.178, H.184, S.185, G.186 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.184, B:G.186, B:Q.187 EDO.36: 2 residues within 4Å: Chain B: T.743, G.744 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.744

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.16: 6 residues within 4Å: Chain A: L.563, L.566, R.569, W.641, Y.674, E.690 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.569 PG4.34: 6 residues within 4Å: Chain B: L.563, L.566, R.569, W.641, Y.674, E.690 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.569

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Larsbrink, J. et al., Structural Enzymology of Cellvibrio Japonicus Agd31B Reveals Alpha-Transglucosylase Activity in Glycoside Hydrolase Family 31. J.Biol.Chem. (2012)

Release Date

2012-11-14

Peptides

ALPHA-GLUCOSIDASE, PUTATIVE, ADG31B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

ALPHA-GLUCOSIDASE, PUTATIVE, ADG31B

Related Entries With Identical Sequence