SMTL ID : 6aq6.1

X-ray crystal structure of Erythrina crista-galli lectin in complex with N-acetyllactosamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x NAG- GAL: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-GAL.1: 10 residues within 4Å: Chain A: A.88, D.89, Y.106, G.107, F.131, N.133, G.217, A.218, Q.219, A.222 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.89, A:G.107, A:N.133, A:N.133, A:A.218, A:Q.219, A:A.218, A:Q.219 NAG-GAL.3: 10 residues within 4Å: Chain B: A.88, D.89, Y.106, G.107, F.131, N.133, G.217, A.218, Q.219, A.222 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.89, B:G.107, B:N.133, B:A.218, B:Q.219

1 x NAG- NAG- BMA- XYP- MAN- FUC: beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)]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-XYP-MAN-FUC.2: 4 residues within 4Å: Chain A: K.101, V.111, N.113, Y.121 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.4: 3 residues within 4Å: Chain B: N.113, D.118, Y.121 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: D.129, F.131, N.133, D.136 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.129, A:D.129, A:F.131, H2O.1, H2O.2 CA.8: 4 residues within 4Å: Chain B: D.129, F.131, N.133, D.136 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.129, B:D.129, B:F.131, B:D.136, H2O.9

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

MN.6: 4 residues within 4Å: Chain A: E.127, D.129, D.136, H.142 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.127, A:D.129, A:D.136, A:H.142, H2O.1, H2O.1 MN.9: 4 residues within 4Å: Chain B: E.127, D.129, D.136, H.142 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.127, B:D.129, B:D.136, B:H.142, H2O.8, H2O.8

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

NA.7: 1 residues within 4Å: Chain A: G.163 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.163 Water bridges: A:S.77, A:S.77, A:Q.164

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.10: 2 residues within 4Å: Chain B: T.155, P.157 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Q.139, B:T.155, B:T.155 ACT.11: 6 residues within 4Å: Chain B: R.73, F.74, S.75, S.230, W.231, S.232 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.75, B:S.230, B:S.232 Water bridges: B:S.230

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sood, A. et al., Defining the Specificity of Carbohydrate-Protein Interactions by Quantifying Functional Group Contributions. J Chem Inf Model (2018)

Release Date

2018-08-22

Peptides

Lectin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lectin

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