SMTL ID : 4ba0.1

Crystal Structure of Agd31B, alpha-transglucosylase, complexed with 5F-alpha-GlcF

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x ARG: ARGININE(Non-covalent)

ARG.1: 4 residues within 4Å: Chain A: R.176, A.177, H.178, Q.187 5 PLIP interactions: 5 interactions with chain A, Hydrogen bonds: A:A.177, A:Q.187 Water bridges: A:R.176, A:G.186 pi-Cation interactions: A:H.178 ARG.13: 4 residues within 4Å: Chain B: R.176, A.177, H.178, Q.187 5 PLIP interactions: 5 interactions with chain B, Hydrogen bonds: B:A.177, B:Q.187 Water bridges: B:R.176, B:G.186 pi-Cation interactions: B:H.178

2 x 5GF: 5-fluoro-beta-D-glucopyranose(Post Translational Modification)

5GF.2: 12 residues within 4Å: Chain A: F.271, D.299, L.300, I.341, W.410, D.412, L.413, R.463, W.477, D.480, F.513, H.540 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.299, A:D.412, A:R.463, A:D.480, A:H.540 Water bridges: A:E.343, A:R.463, A:D.480, A:D.480 5GF.14: 12 residues within 4Å: Chain B: F.271, D.299, L.300, I.341, W.410, D.412, L.413, R.463, W.477, D.480, F.513, H.540 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.299, B:D.412, B:R.463, B:D.480, B:H.540 Water bridges: B:R.463

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

EDO.3: 5 residues within 4Å: Chain A: Q.77, L.78, S.229, G.230, R.231 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.78, A:G.230 EDO.15: 5 residues within 4Å: Chain B: Q.77, L.78, S.229, G.230, R.231 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.78, B:G.230

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

SO4.4: 3 residues within 4Å: Chain A: R.797 Chain B: D.553, E.554 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:E.554 Water bridges: A:R.797, A:R.797 Salt bridges: A:R.797 SO4.5: 4 residues within 4Å: Chain A: R.561, P.562, K.565 Ligands: SO4.17 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.565 SO4.6: 4 residues within 4Å: Chain A: T.323, P.324, L.325, D.326 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.325, A:D.326 Water bridges: A:K.318 SO4.7: 2 residues within 4Å: Chain A: R.58, R.231 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.58, A:R.231 SO4.8: 4 residues within 4Å: Chain A: T.732, D.733, N.734, Q.735 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.732, A:T.732, A:D.733, A:N.734 SO4.9: 6 residues within 4Å: Chain A: T.107, R.123, G.239, N.240, S.244, N.248 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.240, A:N.240, A:S.244, A:N.248 Salt bridges: A:R.123 SO4.10: 4 residues within 4Å: Chain A: T.97, E.98, N.99, H.100 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.97, A:N.99, A:N.99 Salt bridges: A:H.100 SO4.16: 3 residues within 4Å: Chain A: D.553, E.554 Chain B: R.797 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.554 Water bridges: B:R.797, B:R.797 Salt bridges: B:R.797 SO4.17: 4 residues within 4Å: Chain B: R.561, P.562, K.565 Ligands: SO4.5 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.565 SO4.18: 4 residues within 4Å: Chain B: T.323, P.324, L.325, D.326 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.325, B:D.326 Water bridges: B:K.318 SO4.19: 2 residues within 4Å: Chain B: R.58, R.231 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.58, B:R.231 SO4.20: 4 residues within 4Å: Chain B: T.732, D.733, N.734, Q.735 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.732, B:T.732, B:D.733, B:N.734 SO4.21: 6 residues within 4Å: Chain B: T.107, R.123, G.239, N.240, S.244, N.248 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.240, B:N.240, B:S.244, B:N.248 Salt bridges: B:R.123 SO4.22: 4 residues within 4Å: Chain B: T.97, E.98, N.99, H.100 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.97, B:N.99, B:N.99 Salt bridges: B:H.100

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.11: 5 residues within 4Å: Chain A: L.566, R.569, W.641, Y.674, E.690 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.569, A:E.690 PGE.23: 5 residues within 4Å: Chain B: L.566, R.569, W.641, Y.674, E.690 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.569, B:E.690

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.12: 7 residues within 4Å: Chain A: H.731, T.732, D.733, Q.735, S.764, Y.767, K.817 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.767, A:Y.767, A:K.817 Water bridges: A:S.764, A:S.764, A:D.765 PEG.24: 7 residues within 4Å: Chain B: H.731, T.732, D.733, Q.735, S.764, Y.767, K.817 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.731, B:Y.767, B:K.817 Water bridges: B:S.764, B:S.764, B:D.765

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

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