SMTL ID : 4usc.1

Crystal structure of peroxidase from palm tree Chamaerops excelsa

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-MAN.1: 6 residues within 4Å: Chain A: E.78, A.81, N.298, S.300, V.301 Ligands: MAN.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.78, A:S.300

2 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(Non-covalent)

NAG-FUC-NAG.2: 2 residues within 4Å: Chain A: N.267, A.270 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.3: 5 residues within 4Å: Chain B: Q.3, I.4, G.5, N.8, Q.118 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.118

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: S.170, D.223, T.226, V.229, D.231 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:S.170, A:S.170, A:D.223, A:T.226, A:V.229 CA.5: 5 residues within 4Å: Chain A: D.43, V.46, G.48, D.50, S.52 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.43, A:V.46, A:G.48, A:D.50, A:S.52 CA.17: 5 residues within 4Å: Chain B: D.43, V.46, G.48, D.50, S.52 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.43, B:V.46, B:G.48, B:D.50, B:S.52 CA.18: 5 residues within 4Å: Chain B: S.170, D.223, T.226, V.229, D.231 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:S.170, B:S.170, B:D.223, B:T.226, B:V.229

1 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.6: 4 residues within 4Å: Chain A: E.78 Ligands: NAG-NAG-MAN.1, NAG-NAG-MAN.1, NAG-NAG-MAN.1 No protein-ligand interaction detected (PLIP)

5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.7: 4 residues within 4Å: Chain A: I.4, G.5, F.6, N.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.4, A:I.4, A:N.8 NAG.8: 2 residues within 4Å: Chain A: N.127, G.293 No protein-ligand interaction detected (PLIP) NAG.9: 4 residues within 4Å: Chain A: Y.184, N.185, Q.191, S.210 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.185, A:Q.191, A:S.210 NAG.15: 2 residues within 4Å: Chain B: N.267, A.270 No protein-ligand interaction detected (PLIP) NAG.16: 4 residues within 4Å: Chain B: D.56, N.298, S.300, V.301 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.298

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

SO4.10: 4 residues within 4Å: Chain A: R.75, G.76, F.77, E.78 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.76, A:F.77, A:E.78 SO4.19: 4 residues within 4Å: Chain B: R.75, G.76, F.77, E.78 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.76, B:F.77, B:E.78

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

PEG.11: 4 residues within 4Å: Chain A: D.56, K.65, D.66, F.77 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.65

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

HEM.12: 26 residues within 4Å: Chain A: P.34, G.35, I.37, R.38, F.41, S.73, R.75, P.139, A.140, P.141, L.148, F.152, L.165, S.166, A.168, H.169, G.172, V.173, S.174, H.175, S.178, L.222, L.245, S.247, M.282 Ligands: PEO.14 25 PLIP interactions: 25 interactions with chain A, Hydrophobic interactions: 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:F.152, A:L.165, A:L.165, A:A.168, A:L.222, A:L.245 Hydrogen bonds: A:V.173, A:H.175, A:S.178, A:S.178 Water bridges: A:R.75 Salt bridges: A:R.75, A:H.175 pi-Stacking: A:F.41 pi-Cation interactions: A:R.38 Metal complexes: A:H.169 HEM.20: 24 residues within 4Å: Chain B: P.34, G.35, R.38, F.41, S.73, R.75, P.139, A.140, P.141, L.148, F.152, L.165, S.166, A.168, H.169, G.172, V.173, S.174, H.175, S.178, L.222, L.245, S.247, M.282 23 PLIP interactions: 23 interactions with chain B, Hydrophobic interactions: B:R.38, B:F.41, B:F.41, B:F.41, B:P.139, B:L.148, B:F.152, B:L.165, B:L.165, B:A.168, B:L.222, B:L.245 Hydrogen bonds: B:V.173, B:H.175, B:S.178, B:S.178 Water bridges: B:S.73, B:R.75 Salt bridges: B:R.75, B:H.175 pi-Stacking: B:F.41 pi-Cation interactions: B:R.38 Metal complexes: B:H.169

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

EDO.13: 2 residues within 4Å: Chain A: L.240 Chain B: R.233 No protein-ligand interaction detected (PLIP) EDO.21: 1 residues within 4Å: Chain B: Q.239 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.233

1 x PEO: HYDROGEN PEROXIDE(Non-functional Binders)

PEO.14: 4 residues within 4Å: Chain A: R.38, F.41, H.42 Ligands: HEM.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.38, A:H.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bernardes, A. et al., Crystal Structure Analysis of Peroxidase from the Palm Tree Chamaerops Excelsa. Biochimie (2015)

Release Date

2015-05-27

Peptides

PEROXIDASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PEROXIDASE