SMTL ID : 3zvx.1

STRUCTURE OF THE LECTIN FROM PLATYPODIUM ELEGANS IN COMPLEX WITH A TRIMANNOSIDE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

1 x MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose(Non-covalent)

MAN-MAN-MAN.1: 12 residues within 4Å: Chain A: A.94, D.95, G.114, G.115, F.141, A.143, N.145, S.146, N.147, G.229, E.230, Q.231 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.145 Water bridges: A:N.145

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

MN.2: 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.5, H2O.5 MN.7: 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.11, H2O.11

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 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.4, H2O.4 CA.8: 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.10, H2O.10

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

SO4.4: 1 residues within 4Å: Chain A: R.21 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.21 SO4.6: 3 residues within 4Å: Chain A: A.143, Q.144, N.145 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.144, A:N.145, A:N.145 Water bridges: A:N.152

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: P.109, S.110, N.121 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.110, A:N.121 GOL.9: 1 residues within 4Å: Chain B: W.68 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   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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