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

X-ray Crystal Structure of Rattlesnake Venom Complexed With Thiodigalactoside

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-10-mer

Ligands

2 x GAL- YIO: 1-thio-beta-D-galactopyranose-(1-1)-beta-D-galactopyranose(Non-covalent)

GAL-YIO.1: 7 residues within 4Å: Chain B: Q.96, D.98, Y.100, E.104, N.119, D.120 Ligands: CA.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.96, B:E.104, B:N.119 GAL-YIO.15: 7 residues within 4Å: Chain G: Q.96, D.98, Y.100, E.104, N.119, D.120 Ligands: CA.19 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:Q.96, G:E.104, G:N.119

10 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.2: 6 residues within 4Å: Chain A: Q.96, D.98, E.104, N.119, D.120 Ligands: GAL.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.98, A:E.104, A:D.120, A:D.120 CA.5: 6 residues within 4Å: Chain B: Q.96, D.98, E.104, N.119, D.120 Ligands: GAL-YIO.1 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.98, B:E.104, B:D.120, B:D.120 CA.7: 6 residues within 4Å: Chain C: Q.96, D.98, E.104, N.119, D.120 Ligands: GAL.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.98, C:E.104, C:D.120, C:D.120 CA.10: 5 residues within 4Å: Chain D: Q.96, D.98, E.104, N.119, D.120 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.104, D:D.120 CA.12: 6 residues within 4Å: Chain E: Q.96, D.98, E.104, N.119, D.120 Ligands: GAL.14 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.98, E:E.104, E:D.120, E:D.120 CA.16: 6 residues within 4Å: Chain F: Q.96, D.98, E.104, N.119, D.120 Ligands: GAL.18 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.98, F:E.104, F:D.120, F:D.120 CA.19: 6 residues within 4Å: Chain G: Q.96, D.98, E.104, N.119, D.120 Ligands: GAL-YIO.15 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.98, G:E.104, G:D.120, G:D.120 CA.21: 6 residues within 4Å: Chain H: Q.96, D.98, E.104, N.119, D.120 Ligands: GAL.23 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:D.98, H:E.104, H:D.120, H:D.120 CA.24: 5 residues within 4Å: Chain I: Q.96, D.98, E.104, N.119, D.120 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:E.104, I:D.120 CA.26: 6 residues within 4Å: Chain J: Q.96, D.98, E.104, N.119, D.120 Ligands: GAL.28 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-covalent)(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain A: Y.15, S.42, H.44, Q.132 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.42, A:S.42 NA.6: 4 residues within 4Å: Chain B: L.13, Y.15, S.42, Q.132 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.42, B:S.42 Water bridges: B:S.42 NA.8: 4 residues within 4Å: Chain C: L.13, Y.15, S.42, Q.132 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.15, C:S.42, C:S.42 NA.11: 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.13: 4 residues within 4Å: Chain E: L.13, Y.15, S.42, Q.132 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Y.15, E:Y.15, E:S.42 NA.17: 4 residues within 4Å: Chain F: Y.15, S.42, H.44, Q.132 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:Y.15, F:S.42, F:Q.132 NA.20: 4 residues within 4Å: Chain G: L.13, Y.15, S.42, Q.132 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:Y.15, G:S.42, G:Q.132 Water bridges: G:S.42 NA.22: 4 residues within 4Å: Chain H: L.13, Y.15, S.42, Q.132 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:S.42, H:S.42 NA.25: 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:S.42, I:S.42 NA.27: 4 residues within 4Å: Chain J: L.13, Y.15, S.42, Q.132 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:S.42, J:S.42

6 x GAL: beta-D-galactopyranose(Non-covalent)(Non-functional Binders)

GAL.4: 8 residues within 4Å: Chain A: Q.96, D.98, Y.100, E.104, N.119, D.120, Q.121 Ligands: CA.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.96, A:E.104, A:N.119, A:Q.121 Water bridges: A:N.119 GAL.9: 8 residues within 4Å: Chain C: Q.96, D.98, Y.100, E.104, N.119, D.120, Q.121 Ligands: CA.7 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.96, C:E.104 Water bridges: C:Q.121, C:Q.121 GAL.14: 7 residues within 4Å: Chain E: Q.96, D.98, Y.100, E.104, N.119, D.120 Ligands: CA.12 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Q.96, E:E.104, E:N.119, E:N.119, E:Q.121 GAL.18: 8 residues within 4Å: Chain F: Q.96, D.98, Y.100, E.104, N.119, D.120, Q.121 Ligands: CA.16 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:Q.96, F:E.104, F:N.119, F:Q.121 GAL.23: 8 residues within 4Å: Chain H: Q.96, D.98, Y.100, E.104, N.119, D.120, Q.121 Ligands: CA.21 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:Q.96, H:E.104, H:N.119 Water bridges: H:Q.121, H:Q.121 GAL.28: 7 residues within 4Å: Chain J: Q.96, D.98, Y.100, E.104, N.119, D.120 Ligands: CA.26 4 PLIP interactions: 4 interactions with chain J Hydrogen bonds: J:Q.96, J:E.104, J:N.119, J:Q.121

Links

RCSB   PDBe   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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