SMTL ID : 4wn0.1

Xenopus laevis embryonic epidermal lectin in complex with glycerol phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-trimer

Ligands

9 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: E.63, N.65, G.68, D.74 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.63, A:N.65, A:G.68, H2O.2, H2O.3 CA.2: 4 residues within 4Å: Chain A: H.62, G.73, D.109, D.258 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.62, A:D.109, A:D.258, H2O.3, H2O.3 CA.3: 4 residues within 4Å: Chain A: N.236, E.238, E.250 Ligands: G3P.9 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.238, A:E.250, H2O.4, H2O.4 CA.10: 4 residues within 4Å: Chain B: E.63, N.65, G.68, D.74 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.63, B:N.65, B:G.68, H2O.8, H2O.10 CA.11: 4 residues within 4Å: Chain B: H.62, G.73, D.109, D.258 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.62, B:D.109, B:D.258, H2O.9, H2O.10 CA.12: 4 residues within 4Å: Chain B: N.236, E.238, E.250 Ligands: G3P.18 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.238, B:E.250, H2O.10, H2O.10 CA.19: 4 residues within 4Å: Chain C: E.63, N.65, G.68, D.74 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.63, C:N.65, C:G.68, H2O.14, H2O.16 CA.20: 4 residues within 4Å: Chain C: H.62, G.73, D.109, D.258 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.62, C:D.109, C:D.258, H2O.16, H2O.16 CA.21: 4 residues within 4Å: Chain C: N.236, E.238, E.250 Ligands: G3P.27 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.238, C:E.250, H2O.16, H2O.17

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 2 residues within 4Å: Chain A: R.138, R.144 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.138 Salt bridges: A:R.138, A:R.144 PO4.13: 2 residues within 4Å: Chain B: R.138, R.144 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.138 Salt bridges: B:R.138, B:R.144 PO4.22: 2 residues within 4Å: Chain C: R.138, R.144 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.138 Salt bridges: C:R.138, C:R.144

12 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.5: 5 residues within 4Å: Chain A: P.87, E.88, K.169, D.171, I.172 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.169, A:D.171 1PE.6: 4 residues within 4Å: Chain A: S.205, F.207, T.208, K.233 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.231, A:K.233 1PE.7: 7 residues within 4Å: Chain A: S.141, I.142, Y.187, D.188, L.189, G.190, K.194 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.190, A:K.194 1PE.8: 7 residues within 4Å: Chain A: F.67, K.69, P.253, R.254, D.263, W.264, G.266 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.266 Water bridges: A:R.254 1PE.14: 5 residues within 4Å: Chain B: P.87, E.88, K.169, D.171, I.172 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.169, B:D.171 1PE.15: 4 residues within 4Å: Chain B: S.205, F.207, T.208, K.233 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.231, B:K.233 1PE.16: 7 residues within 4Å: Chain B: S.141, I.142, Y.187, D.188, L.189, G.190, K.194 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.190, B:K.194 1PE.17: 7 residues within 4Å: Chain B: F.67, K.69, P.253, R.254, D.263, W.264, G.266 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.266 Water bridges: B:R.254 1PE.23: 5 residues within 4Å: Chain C: P.87, E.88, K.169, D.171, I.172 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.169, C:D.171 1PE.24: 4 residues within 4Å: Chain C: S.205, F.207, T.208, K.233 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.231, C:K.233 1PE.25: 7 residues within 4Å: Chain C: S.141, I.142, Y.187, D.188, L.189, G.190, K.194 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.190, C:K.194 1PE.26: 7 residues within 4Å: Chain C: F.67, K.69, P.253, R.254, D.263, W.264, G.266 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.266 Water bridges: C:R.254

3 x G3P: SN-GLYCEROL-3-PHOSPHATE(Non-covalent)

G3P.9: 7 residues within 4Å: Chain A: N.236, E.238, H.239, E.250, W.264, W.273 Ligands: CA.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.236, A:W.273 G3P.18: 7 residues within 4Å: Chain B: N.236, E.238, H.239, E.250, W.264, W.273 Ligands: CA.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.236, B:H.239, B:W.273 G3P.27: 7 residues within 4Å: Chain C: N.236, E.238, H.239, E.250, W.264, W.273 Ligands: CA.21 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.236, C:W.273

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Wangkanont, K. et al., Structures of Xenopus Embryonic Epidermal Lectin Reveal a Conserved Mechanism of Microbial Glycan Recognition. J.Biol.Chem. (2016)

Release Date

2016-01-20

Peptides

XEEL protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

XEEL protein

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