SMTL ID : 3qlq.1

Crystal structure of Concanavalin A bound to an octa-alpha-mannosyl-octasilsesquioxane cluster

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.10, A:Y.12, A:D.19, H2O.2, H2O.2 CA.5: 4 residues within 4Å: Chain B: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.10, B:Y.12, B:D.19, H2O.4, H2O.5 CA.8: 4 residues within 4Å: Chain C: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.10, C:Y.12, C:D.19, H2O.6, H2O.8 CA.10: 4 residues within 4Å: Chain D: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.10, D:Y.12, D:D.19, H2O.9, H2O.9

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 5 residues within 4Å: Chain A: E.8, D.10, D.19, H.24, S.34 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.8, A:D.10, A:D.19, A:H.24, H2O.1, H2O.3 MN.4: 4 residues within 4Å: Chain B: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.8, B:D.10, B:D.19, B:H.24, H2O.4, H2O.5 MN.7: 4 residues within 4Å: Chain C: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.8, C:D.10, C:D.19, C:H.24, H2O.6, H2O.8 MN.11: 4 residues within 4Å: Chain D: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.8, D:D.10, D:D.19, D:H.24, H2O.9, H2O.10

4 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.3: 9 residues within 4Å: Chain A: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.14, A:N.14, A:L.99, A:Y.100, A:Y.100, A:R.228 MAN.6: 9 residues within 4Å: Chain B: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.14, B:L.99, B:Y.100, B:Y.100, B:R.228 MAN.9: 9 residues within 4Å: Chain C: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.14, C:L.99, C:Y.100, C:Y.100, C:R.228 MAN.12: 9 residues within 4Å: Chain D: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.14, D:L.99, D:Y.100, D:Y.100, D:R.228

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Trastoy, B. et al., Synthesis and Biophysical Study of Disassembling Nano hybrid Bioconjugates with a Cubic Octasilsesquioxane Core. Adv Funct Mater (2012)

Release Date

2012-02-08

Peptides

Concanavalin-A: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Concanavalin-A

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