SMTL ID : 4cuo.1

Banyan peroxidase with glycosylation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

homo-dimer

Ligands

2 x NAG- FUC: alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 4 residues within 4Å: Chain A: Q.66, N.71, N.72, R.131 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.66 Hydrogen bonds: A:N.71, A:N.72 NAG-FUC.22: 4 residues within 4Å: Chain B: Q.66, N.71, N.72, R.131 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Q.66 Hydrogen bonds: B:N.71, B:N.72

2 x NAG- NAG- BMA- XYS- MAN- MAN- FUC: alpha-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-XYS-MAN-MAN-FUC.2: 3 residues within 4Å: Chain A: N.130, L.133, Q.136 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.136 NAG-NAG-BMA-XYS-MAN-MAN-FUC.23: 3 residues within 4Å: Chain B: N.130, L.133, Q.136 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.136

4 x NAG- FUC- NAG: alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUC-NAG.3: 5 residues within 4Å: Chain A: N.158, T.160, A.277, K.281 Ligands: NAG.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.277 NAG-FUC-NAG.4: 6 residues within 4Å: Chain A: N.197, Q.237, T.238, Q.239, Y.240 Ligands: SO4.16 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.24: 5 residues within 4Å: Chain B: N.158, T.160, A.277, K.281 Ligands: NAG.29 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.277 NAG-FUC-NAG.25: 6 residues within 4Å: Chain B: N.197, Q.237, T.238, Q.239, Y.240 Ligands: SO4.37 No protein-ligand interaction detected (PLIP)

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.5: 28 residues within 4Å: Chain A: R.31, A.34, S.35, I.37, R.38, F.41, S.73, R.75, P.139, S.140, P.141, L.148, F.152, L.162, L.165, S.166, A.168, H.169, F.171, G.172, R.173, A.174, Q.175, F.178, L.220, L.243, T.245 Ligands: CL.12 29 PLIP interactions: 29 interactions with chain A, Hydrophobic interactions: A:A.34, A:I.37, A:R.38, A:F.41, A:F.41, A:F.41, A:P.139, A:P.141, A:L.148, A:F.152, A:L.162, A:L.165, A:A.168, A:F.171, A:A.174, A:F.178, A:F.178, A:F.178, A:L.220 Hydrogen bonds: A:R.31, A:R.173, A:Q.175, A:Q.175 Water bridges: A:R.38 Salt bridges: A:R.31, A:R.38 pi-Stacking: A:F.41 pi-Cation interactions: A:R.38 Metal complexes: A:H.169 HEM.26: 28 residues within 4Å: Chain B: R.31, A.34, S.35, I.37, R.38, F.41, S.73, R.75, P.139, S.140, P.141, L.148, F.152, L.162, L.165, S.166, A.168, H.169, F.171, G.172, R.173, A.174, Q.175, F.178, L.220, L.243, T.245 Ligands: CL.33 29 PLIP interactions: 29 interactions with chain B, Hydrophobic interactions: B:A.34, B:I.37, B:R.38, B:F.41, B:F.41, B:F.41, B:P.139, B:P.141, B:L.148, B:F.152, B:L.162, B:L.165, B:A.168, B:F.171, B:A.174, B:F.178, B:F.178, B:F.178, B:L.220 Hydrogen bonds: B:R.31, B:R.173, B:Q.175, B:Q.175 Water bridges: B:R.38 Salt bridges: B:R.31, B:R.38 pi-Stacking: B:F.41 pi-Cation interactions: B:R.38 Metal complexes: B:H.169

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

NAG.6: 3 residues within 4Å: Chain A: N.185, A.188, G.190 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.189 NAG.7: 4 residues within 4Å: Chain A: N.213, S.215, T.216 Chain B: P.209 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.209 Water bridges: B:N.213 NAG.8: 5 residues within 4Å: Chain A: K.149, T.159, N.256, I.260 Ligands: NAG-FUC-NAG.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.260 Hydrogen bonds: A:K.149, A:N.256 NAG.27: 3 residues within 4Å: Chain B: N.185, A.188, G.190 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.189 NAG.28: 4 residues within 4Å: Chain A: P.209 Chain B: N.213, S.215, T.216 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.209 Water bridges: A:N.213 NAG.29: 5 residues within 4Å: Chain B: K.149, T.159, N.256, I.260 Ligands: NAG-FUC-NAG.24 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.260 Hydrogen bonds: B:K.149, B:T.159, B:N.256

4 x CA: CALCIUM ION(Non-covalent)

CA.9: 5 residues within 4Å: Chain A: T.170, D.221, T.224, A.227, D.229 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.170, A:D.221, A:T.224, A:T.224, A:A.227 CA.10: 6 residues within 4Å: Chain A: D.43, V.46, G.48, D.50, S.52 Ligands: NA.11 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.43, A:D.43, A:V.46, A:G.48, A:D.50 CA.30: 5 residues within 4Å: Chain B: T.170, D.221, T.224, A.227, D.229 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:T.170, B:D.221, B:T.224, B:T.224, B:A.227 CA.31: 6 residues within 4Å: Chain B: D.43, V.46, G.48, D.50, S.52 Ligands: NA.32 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.43, B:D.43, B:V.46, B:G.48, B:D.50

2 x NA: SODIUM ION(Non-functional Binders)

NA.11: 6 residues within 4Å: Chain A: D.43, V.46, G.48, D.50, S.52 Ligands: CA.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.43, A:D.50, A:D.50, A:S.52 NA.32: 6 residues within 4Å: Chain B: D.43, V.46, G.48, D.50, S.52 Ligands: CA.31 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.43, B:D.50, B:S.52

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.12: 4 residues within 4Å: Chain A: R.38, F.41, H.42 Ligands: HEM.5 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain A: T.218, N.219 Chain B: T.203, N.206 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain A: T.102, W.117, P.120, M.279, I.280 Ligand excluded by PLIP CL.33: 4 residues within 4Å: Chain B: R.38, F.41, H.42 Ligands: HEM.26 Ligand excluded by PLIP CL.34: 4 residues within 4Å: Chain A: T.203, N.206 Chain B: T.218, N.219 Ligand excluded by PLIP CL.35: 5 residues within 4Å: Chain B: T.102, W.117, P.120, M.279, I.280 Ligand excluded by PLIP

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

SO4.15: 4 residues within 4Å: Chain A: R.75, G.76, F.77, D.78 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.76, A:F.77, A:D.78, A:D.78 Water bridges: A:A.74, A:V.79 SO4.16: 4 residues within 4Å: Chain A: N.197, T.198 Ligands: NAG-FUC-NAG.4, NAG-FUC-NAG.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.197, A:T.198 Water bridges: A:Q.239 SO4.17: 1 residues within 4Å: Chain A: R.205 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Y.184, A:R.205 Salt bridges: A:R.205 SO4.36: 4 residues within 4Å: Chain B: R.75, G.76, F.77, D.78 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.76, B:F.77, B:D.78, B:D.78 Water bridges: B:A.74, B:V.79 SO4.37: 4 residues within 4Å: Chain B: N.197, T.198 Ligands: NAG-FUC-NAG.25, NAG-FUC-NAG.25 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.197, B:T.198 Water bridges: B:T.199, B:Q.239 SO4.38: 1 residues within 4Å: Chain B: R.205 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:D.29, B:Y.184, B:Y.184 Salt bridges: B:R.205

8 x CO3: CARBONATE ION(Non-functional Binders)

CO3.18: 4 residues within 4Å: Chain A: T.15, S.16, R.19, Q.107 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.16, A:R.19, A:Q.107 Water bridges: A:T.15, A:E.106, A:E.106, A:Q.107 CO3.19: 3 residues within 4Å: Chain A: N.284, I.285, G.286 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.286 CO3.20: 1 residues within 4Å: Chain A: R.75 No protein-ligand interaction detected (PLIP) CO3.21: 4 residues within 4Å: Chain A: T.224, P.225, D.226, A.227 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.226, A:A.227 Water bridges: B:T.199 CO3.39: 4 residues within 4Å: Chain B: T.15, S.16, R.19, Q.107 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.16, B:R.19, B:Q.107 Water bridges: B:T.15, B:E.106, B:E.106, B:Q.107 CO3.40: 3 residues within 4Å: Chain B: N.284, I.285, G.286 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.286 CO3.41: 1 residues within 4Å: Chain B: R.75 No protein-ligand interaction detected (PLIP) CO3.42: 4 residues within 4Å: Chain B: T.224, P.225, D.226, A.227 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.226, B:A.227 Water bridges: A:T.199

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Palm, G.J. et al., Post-Translational Modification and Extended Glycosylation Pattern of a Plant Latex Peroxidase of Native Source Characterized by X-Ray Crystallography. FEBS J. (2014)

Release Date

2014-07-23

Peptides

BANYAN PEROXIDASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

BANYAN PEROXIDASE