SMTL ID : 4wmo.2 (1 other biounit)

Selenomethionine derivative of Xenopus laevis embryonic epidermal lectin carbohydrate-binding domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

9 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: N.236, E.238, E.250 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.238, A:E.250, H2O.3, H2O.3, H2O.6 CA.2: 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:N.65, A:G.68, A:D.74, H2O.2, H2O.5 CA.3: 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.9 CA.7: 3 residues within 4Å: Chain B: N.236, E.238, E.250 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.238, B:E.250, H2O.9, H2O.11, H2O.11 CA.8: 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.11, H2O.18 CA.9: 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.12, H2O.18 CA.12: 3 residues within 4Å: Chain C: N.236, E.238, E.250 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.238, C:E.250, H2O.20, H2O.21, H2O.27 CA.13: 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.28, H2O.29 CA.14: 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:N.65, C:G.68, C:D.74, H2O.20, H2O.27

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

1PE.4: 4 residues within 4Å: Chain A: E.88, K.169, D.171, I.172 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.169 1PE.5: 6 residues within 4Å: Chain A: R.204, S.205, F.207, T.208, K.231, K.233 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.208, A:K.231, A:K.231, A:K.233 1PE.6: 2 residues within 4Å: Chain A: K.174, C.175 No protein-ligand interaction detected (PLIP) 1PE.10: 7 residues within 4Å: Chain B: P.87, E.88, P.167, K.169, Y.170, D.171, I.172 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.88, B:K.169 Water bridges: B:K.169, B:Y.170 1PE.11: 4 residues within 4Å: Chain B: C.175, L.176, S.205, K.233 3 PLIP interactions: 3 interactions with chain B Water bridges: B:C.175, B:S.219, B:C.235 1PE.15: 5 residues within 4Å: Chain C: P.87, E.88, K.169, D.171, I.172 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.88, C:E.88, C:E.88, C:K.169 1PE.16: 5 residues within 4Å: Chain C: S.205, F.207, T.208, K.231, K.233 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.233 Water bridges: C:K.231 1PE.17: 4 residues within 4Å: Chain C: K.174, C.175, K.233, C.235 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.174 Water bridges: C:C.235

Links

RCSB   PDBe   PDBe-KB   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
C

B
B

C
A

XEEL protein

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