SMTL ID : 5zc0.2 (1 other biounit)

Crystal structure of Xenopus embryonic epidermal lectin in complex with Samarium ions

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-trimer

Ligands

6 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.1, H2O.1 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.1, H2O.1 CA.7: 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.2, H2O.2 CA.8: 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.2, H2O.2 CA.13: 5 residues within 4Å: Chain C: E.63, N.64, 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.3, H2O.3 CA.14: 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.2, H2O.3

12 x SM: SAMARIUM (III) ION(Non-covalent)(Non-functional Binders)

SM.3: 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.1, H2O.1, H2O.1 SM.4: 3 residues within 4Å: Chain A: E.119, G.156, E.161 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.119, A:E.119, A:G.156, A:E.161 SM.5: 1 residues within 4Å: Chain A: E.37 No protein-ligand interaction detected (PLIP) SM.6: 2 residues within 4Å: Chain A: E.37, D.38 No protein-ligand interaction detected (PLIP) SM.9: 3 residues within 4Å: Chain B: N.236, E.238, E.250 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.238, B:E.250, B:E.250, H2O.1, H2O.2 SM.10: 3 residues within 4Å: Chain B: E.119, G.156, E.161 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.119, B:E.119, B:G.156, B:E.161, B:E.161 SM.11: 1 residues within 4Å: Chain B: E.37 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.37 SM.12: 2 residues within 4Å: Chain B: E.37, D.38 No protein-ligand interaction detected (PLIP) SM.15: 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.3, H2O.3, H2O.3 SM.16: 3 residues within 4Å: Chain C: E.119, G.156, E.161 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.119, C:E.119, C:G.156 SM.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SM.18: 1 residues within 4Å: Chain C: E.37 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kozak, J.J. et al., Structural stabilities of calcium proteins: Human intelectin-1 and frog lectin XEEL. J. Inorg. Biochem. (2018)

Release Date

2018-06-06

Peptides

Xenopus Embryonic Epidermal Lectin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

Xenopus Embryonic Epidermal Lectin

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