SMTL ID : 3zyr.1

Structure of the lectin from Platypodium elegans in complex with heptasaccharide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- MAN- NAG- MAN- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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(Non-functional Binders)

NAG-NAG-BMA-MAN-NAG-MAN-NAG.1: 22 residues within 4Å: Chain A: R.53, S.54, L.90, S.91, N.92, A.94, D.95, G.111, A.113, G.114, G.115, L.116, F.141, A.143, N.145, S.146, N.147, S.228, G.229, E.230, Q.231 Ligands: ASN.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.145, A:S.146, A:S.146, A:Q.231, A:Q.231, A:G.115, A:N.147, A:N.147, A:G.229, A:E.230, A:Q.231, A:Q.231 Hydrophobic interactions: A:E.230 Water bridges: A:S.54, A:S.54, A:A.113, A:A.113, A:E.230, A:E.230 NAG-NAG-BMA-MAN-NAG-MAN-NAG.2: 21 residues within 4Å: Chain B: R.53, S.54, L.90, S.91, N.92, A.94, D.95, G.111, A.113, G.114, G.115, L.116, F.141, A.143, N.145, S.146, N.147, G.229, E.230, Q.231 Ligands: GOL.12 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.145, B:S.146, B:Q.231, B:Q.231, B:G.115, B:N.147, B:N.147, B:G.229, B:E.230, B:Q.231, B:Q.231 Water bridges: B:E.230, B:S.54, B:G.111, B:A.113 Hydrophobic interactions: B:E.230

1 x ASN: ASPARAGINE(Non-functional Binders)

ASN.3: 1 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-NAG-MAN-NAG.1 No protein-ligand interaction detected (PLIP)

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.4: 4 residues within 4Å: Chain A: E.137, D.139, D.150, H.155 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.137, A:D.139, A:D.150, A:H.155, H2O.7, H2O.7 MN.10: 4 residues within 4Å: Chain B: E.137, D.139, D.150, H.155 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.137, B:D.139, B:D.150, B:H.155, H2O.16, H2O.16

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: D.139, F.141, N.147, D.150 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.139, A:F.141, A:D.150, H2O.6, H2O.6 CA.11: 4 residues within 4Å: Chain B: D.139, F.141, N.147, D.150 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.139, B:F.141, B:D.150, H2O.15, H2O.16

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: D.10, S.11, Q.64, R.66, W.219 Chain B: E.23, N.25 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.23, B:N.25 Water bridges: B:S.15, A:R.66, A:S.244 GOL.8: 7 residues within 4Å: Chain A: R.58, A.102, T.106, L.119, N.131, Q.132, V.133 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.58, A:T.106, A:N.131, A:Q.132 Water bridges: A:T.107, A:T.107 GOL.9: 6 residues within 4Å: Chain A: I.108, P.109, S.110, G.111, S.112, A.113 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.111 Water bridges: A:P.109, A:A.113 GOL.12: 5 residues within 4Å: Chain B: A.143, Q.144, N.145, N.152 Ligands: NAG-NAG-BMA-MAN-NAG-MAN-NAG.2 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.144, B:N.145, B:N.152, B:N.152

2 x URE: UREA(Non-functional Binders)

URE.7: 2 residues within 4Å: Chain A: W.149, R.164 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.149, A:R.164 Water bridges: A:S.165 URE.13: 5 residues within 4Å: Chain A: N.25 Chain B: Q.64, V.65, R.66, W.219 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:N.25, B:Q.64, B:R.66 Water bridges: A:S.15, B:S.11, B:S.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Benevides, R.G. et al., A Lectin from Platypodium Elegans with Unusual Specificity and Affinity for Asymmetric Complex N-Glycans. J.Biol.Chem. (2012)

Release Date

2012-01-11

Peptides

LECTIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

LECTIN

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