SMTL ID : 7x36.1

Crystal Structure of hetero-Diels-Alderase EupfF

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-tetramer

Ligands

10 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain A: N.45, Y.342, S.343, K.352 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain A: P.187, P.189, D.208, Y.209, A.210, N.213 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: N.45, Y.342, S.343, K.352 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.342 Hydrogen bonds: B:S.343 NAG-NAG.5: 4 residues within 4Å: Chain B: P.67, N.68, N.89, D.91 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain B: P.187, P.189, D.208, Y.209, A.210, N.213 1 PLIP interactions: 1 interactions with chain B Water bridges: B:P.187 NAG-NAG.7: 8 residues within 4Å: Chain B: D.283, L.284, S.297, K.299, N.300, T.302, H.366, L.367 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.284 Hydrogen bonds: B:L.367 Water bridges: B:E.282 NAG-NAG.10: 4 residues within 4Å: Chain D: N.45, Y.342, S.343, K.352 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.342 NAG-NAG.11: 4 residues within 4Å: Chain D: P.67, N.68, N.89, D.91 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 7 residues within 4Å: Chain D: P.187, P.189, D.208, Y.209, A.210, N.213 Ligands: MAN.40 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 8 residues within 4Å: Chain D: D.283, L.284, S.297, K.299, N.300, H.366, L.367, H.368 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.284 Hydrogen bonds: D:L.367

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 7 residues within 4Å: Chain A: D.283, L.284, S.297, K.299, N.300, H.366, L.367 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.284 Hydrogen bonds: A:H.366, A:L.367 NAG-NAG-BMA.9: 7 residues within 4Å: Chain C: D.283, L.284, S.297, N.300, T.302, H.366, L.367 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.284, C:L.367 Hydrogen bonds: C:L.367 Water bridges: C:H.368

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.8: 6 residues within 4Å: Chain C: P.187, P.189, D.208, Y.209, A.210, N.213 No protein-ligand interaction detected (PLIP)

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.14: 5 residues within 4Å: Chain A: P.67, N.68, N.89, D.91 Ligands: EDO.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.89, A:D.91 NAG.30: 3 residues within 4Å: Chain C: N.45, Y.342, K.352 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.352 NAG.31: 5 residues within 4Å: Chain C: P.67, N.68, N.89, D.91 Ligands: EDO.22 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:P.67 Hydrogen bonds: C:N.68, C:N.89, C:D.91 NAG.32: 3 residues within 4Å: Chain C: V.309, N.314, V.344 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.309, C:V.344 Hydrogen bonds: C:N.314

4 x CA: CALCIUM ION(Non-covalent)

CA.15: 4 residues within 4Å: Chain A: E.50, Q.156, N.225, D.273 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.50, A:D.273, H2O.3, H2O.4, H2O.9 CA.25: 4 residues within 4Å: Chain B: E.50, Q.156, N.225, D.273 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.50, B:D.273, H2O.14, H2O.16, H2O.21 CA.33: 4 residues within 4Å: Chain C: E.50, Q.156, N.225, D.273 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.50, C:D.273, H2O.29, H2O.29, H2O.31 CA.37: 4 residues within 4Å: Chain D: E.50, Q.156, N.225, D.273 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.50, D:D.273, H2O.37, H2O.39, H2O.40

3 x BEZ: BENZOIC ACID(Non-covalent)

BEZ.16: 7 residues within 4Å: Chain A: W.48, E.50, S.65, R.96, I.98, F.115, Q.156 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.48, A:W.48, A:F.115 Hydrogen bonds: A:S.65 Salt bridges: A:R.96 BEZ.26: 9 residues within 4Å: Chain B: W.48, E.50, S.65, R.96, I.98, F.115, L.154, Q.156 Ligands: PEG.29 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.115, B:L.154, B:L.154 Hydrogen bonds: B:E.50, B:S.65 Salt bridges: B:R.96 BEZ.34: 7 residues within 4Å: Chain C: W.48, E.50, S.65, R.96, I.98, F.115, Q.156 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:W.48, C:W.48, C:F.115 Hydrogen bonds: C:S.65 Salt bridges: C:R.96 pi-Stacking: C:Y.174

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

EDO.17: 4 residues within 4Å: Chain A: S.269, L.271, L.290, L.348 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.269 EDO.18: 3 residues within 4Å: Chain A: W.193, E.203, L.204 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.204 Water bridges: A:Y.202, A:Y.202 EDO.19: 2 residues within 4Å: Chain A: E.92 Ligands: EDO.24 5 PLIP interactions: 5 interactions with chain A Water bridges: A:Y.88, A:N.89, A:E.92, A:E.92, A:E.92 EDO.20: 4 residues within 4Å: Chain A: G.46, T.66, P.67, P.118 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.46 EDO.21: 3 residues within 4Å: Chain A: K.138, E.139, P.140 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.139 EDO.22: 2 residues within 4Å: Chain A: V.183 Ligands: NAG.31 No protein-ligand interaction detected (PLIP) EDO.23: 5 residues within 4Å: Chain A: N.68, L.86, N.89 Ligands: NAG.14, EDO.24 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.68, A:N.89 EDO.24: 4 residues within 4Å: Chain A: Y.88, N.89 Ligands: EDO.19, EDO.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.89 Water bridges: A:A.87 EDO.27: 3 residues within 4Å: Chain B: W.193, E.203, L.204 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.204 Water bridges: B:E.151, B:E.151 EDO.28: 3 residues within 4Å: Chain B: P.34, P.36, E.37 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.34, B:E.37, B:E.37 EDO.35: 5 residues within 4Å: Chain C: L.290, N.291, G.319, L.341, P.345 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.291 Water bridges: C:N.291, C:G.319 EDO.36: 2 residues within 4Å: Chain C: W.185, P.220 No protein-ligand interaction detected (PLIP) EDO.39: 3 residues within 4Å: Chain D: T.207, D.208, Y.209 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.207

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

PEG.29: 4 residues within 4Å: Chain B: W.48, A.120, N.340 Ligands: BEZ.26 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.120, B:N.340 Water bridges: B:N.340 PEG.41: 6 residues within 4Å: Chain D: S.343, V.344, P.345, D.346, D.350, V.351 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.343, D:D.350 Water bridges: D:K.352 PEG.42: 4 residues within 4Å: Chain D: W.48, A.120, Y.121 Ligands: GOL.38 4 PLIP interactions: 4 interactions with chain D Water bridges: D:A.120, D:S.122, D:N.340, D:N.340

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.38: 5 residues within 4Å: Chain D: F.115, Q.156, Y.174, V.222 Ligands: PEG.42 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.156, D:Q.156 Water bridges: D:R.96, D:N.225

1 x MAN: alpha-D-mannopyranose(Non-functional Binders)

MAN.40: 1 residues within 4Å: Ligands: NAG-NAG.12 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, J. et al., Calcium-dependent glycosylated enzyme in the tandem hetero-Diels-Alder reaction. To Be Published

Release Date

2023-04-05

Peptides

EupfF: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

EupfF