SMTL ID : 1jzn.1 (1 other biounit)

crystal structure of a galactose-specific C-type lectin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-10-mer

Ligands

10 x BGC- GAL: beta-D-galactopyranose-(1-4)-beta-D-glucopyranose(Non-covalent)

BGC-GAL.1: 7 residues within 4Å: Chain A: Q.96, D.98, Y.100, E.104, N.119, D.120 Ligands: CA.6 5 PLIP interactions: 5 interactions with chain A Water bridges: A:Q.96, A:E.108 Hydrogen bonds: A:Q.96, A:E.104, A:N.119, A:Q.121 BGC-GAL.2: 7 residues within 4Å: Chain B: Q.96, D.98, Y.100, E.104, N.119, D.120 Ligands: CA.8 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.94, B:Q.96 Hydrogen bonds: B:Q.96, B:E.104, B:N.119, B:Q.121 BGC-GAL.3: 8 residues within 4Å: Chain C: Q.96, D.98, Y.100, E.104, N.119, D.120, Q.121 Ligands: CA.11 4 PLIP interactions: 4 interactions with chain C Water bridges: C:Q.96, C:Q.96 Hydrogen bonds: C:Q.96, C:E.104, C:N.119, C:Q.121 BGC-GAL.4: 8 residues within 4Å: Chain D: Q.96, D.98, Y.100, E.104, N.119, D.120, Q.121 Ligands: CA.13 5 PLIP interactions: 5 interactions with chain D Water bridges: D:Q.96, D:E.108 Hydrogen bonds: D:Q.96, D:E.104, D:N.119, D:Q.121 BGC-GAL.5: 7 residues within 4Å: Chain E: Q.96, D.98, Y.100, E.104, N.119, D.120 Ligands: CA.15 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:Q.96, E:E.104, E:N.119 Water bridges: E:E.108, E:Q.121, E:Q.121 BGC-GAL.17: 7 residues within 4Å: Chain F: Q.96, D.98, Y.100, E.104, N.119, D.120 Ligands: CA.22 6 PLIP interactions: 6 interactions with chain F Water bridges: F:Q.96, F:E.108, F:E.108 Hydrogen bonds: F:Q.96, F:E.104, F:N.119, F:Q.121 BGC-GAL.18: 7 residues within 4Å: Chain G: Q.96, D.98, Y.100, E.104, N.119, D.120 Ligands: CA.24 4 PLIP interactions: 4 interactions with chain G Water bridges: G:K.94, G:Q.96 Hydrogen bonds: G:Q.96, G:E.104, G:N.119, G:Q.121 BGC-GAL.19: 8 residues within 4Å: Chain H: Q.96, D.98, Y.100, E.104, N.119, D.120, Q.121 Ligands: CA.27 4 PLIP interactions: 4 interactions with chain H Water bridges: H:Q.96, H:Q.96 Hydrogen bonds: H:Q.96, H:E.104, H:N.119, H:Q.121 BGC-GAL.20: 8 residues within 4Å: Chain I: Q.96, D.98, Y.100, E.104, N.119, D.120, Q.121 Ligands: CA.29 5 PLIP interactions: 5 interactions with chain I Water bridges: I:Q.96, I:E.108 Hydrogen bonds: I:Q.96, I:E.104, I:N.119, I:Q.121 BGC-GAL.21: 7 residues within 4Å: Chain J: Q.96, D.98, Y.100, E.104, N.119, D.120 Ligands: CA.31 6 PLIP interactions: 6 interactions with chain J Hydrogen bonds: J:Q.96, J:E.104, J:N.119 Water bridges: J:E.108, J:Q.121, J:Q.121

10 x CA: CALCIUM ION(Non-covalent)

CA.6: 6 residues within 4Å: Chain A: Q.96, D.98, E.104, N.119, D.120 Ligands: BGC-GAL.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.98, A:E.104, A:D.120, A:D.120 CA.8: 6 residues within 4Å: Chain B: Q.96, D.98, E.104, N.119, D.120 Ligands: BGC-GAL.2 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.98, B:E.104, B:D.120, B:D.120 CA.11: 6 residues within 4Å: Chain C: Q.96, D.98, E.104, N.119, D.120 Ligands: BGC-GAL.3 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.98, C:E.104, C:D.120, C:D.120 CA.13: 6 residues within 4Å: Chain D: Q.96, D.98, E.104, N.119, D.120 Ligands: BGC-GAL.4 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.98, D:E.104, D:D.120, D:D.120 CA.15: 6 residues within 4Å: Chain E: Q.96, D.98, E.104, N.119, D.120 Ligands: BGC-GAL.5 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.98, E:E.104, E:D.120, E:D.120 CA.22: 6 residues within 4Å: Chain F: Q.96, D.98, E.104, N.119, D.120 Ligands: BGC-GAL.17 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.98, F:E.104, F:D.120, F:D.120 CA.24: 6 residues within 4Å: Chain G: Q.96, D.98, E.104, N.119, D.120 Ligands: BGC-GAL.18 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.98, G:E.104, G:D.120, G:D.120 CA.27: 6 residues within 4Å: Chain H: Q.96, D.98, E.104, N.119, D.120 Ligands: BGC-GAL.19 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:D.98, H:E.104, H:D.120, H:D.120 CA.29: 6 residues within 4Å: Chain I: Q.96, D.98, E.104, N.119, D.120 Ligands: BGC-GAL.20 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:D.98, I:E.104, I:D.120, I:D.120 CA.31: 6 residues within 4Å: Chain J: Q.96, D.98, E.104, N.119, D.120 Ligands: BGC-GAL.21 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:D.98, J:E.104, J:D.120, J:D.120

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

NA.7: 3 residues within 4Å: Chain A: Y.15, S.42, Q.132 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.42, A:S.42 NA.9: 4 residues within 4Å: Chain B: L.13, Y.15, S.42, Q.132 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.42, B:S.42 NA.12: 3 residues within 4Å: Chain C: Y.15, S.42, Q.132 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.42, C:Q.132 NA.14: 4 residues within 4Å: Chain D: L.13, Y.15, S.42, Q.132 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.15, D:S.42, D:S.42 NA.16: 4 residues within 4Å: Chain E: L.13, Y.15, S.42, Q.132 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Y.15, E:S.42, E:S.42 Water bridges: E:Q.132 NA.23: 3 residues within 4Å: Chain F: Y.15, S.42, Q.132 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:Y.15, F:S.42, F:S.42 NA.25: 4 residues within 4Å: Chain G: L.13, Y.15, S.42, Q.132 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:Y.15, G:S.42, G:Q.132 NA.28: 3 residues within 4Å: Chain H: Y.15, S.42, Q.132 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:Y.15, H:Y.15, H:S.42 NA.30: 4 residues within 4Å: Chain I: L.13, Y.15, S.42, Q.132 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:Y.15, I:S.42 NA.32: 4 residues within 4Å: Chain J: L.13, Y.15, S.42, Q.132 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:S.42, J:Q.132 Water bridges: J:Q.132

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 4 residues within 4Å: Chain B: R.45, Y.46 Chain J: R.45, Y.46 Ligand excluded by PLIP CL.26: 4 residues within 4Å: Chain E: R.45, Y.46 Chain G: R.45, Y.46 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Walker, J.R. et al., X-ray Crystal Structure of a Galactose-Specific C-Type Lectin Possessing a Novel Decameric Quaternary Structure. Biochemistry (2004)

Release Date

2003-07-01

Peptides

Galactose-specific lectin: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
A

G
B

H
C

I
D

J
E

Galactose-specific lectin

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