SMTL ID : 4pf5.1

Crystal structure of Concanavalin A complexed with a synthetic derivative of high-mannose chain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: E.8, D.10, D.19, H.24 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.2, H2O.2 MN.2: 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:D.10, A:D.19, H2O.2, H2O.2 MN.6: 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.6, H2O.6 MN.7: 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.6, H2O.6 MN.9: 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.11, H2O.11 MN.10: 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:D.10, C:D.19, H2O.11, H2O.11 MN.14: 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.15, H2O.15 MN.15: 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.15, H2O.15

4 x M3N: 4-(hydroxymethyl)-1-(alpha-D-mannopyranosyl)-1H-1,2,3-triazole(Non-covalent)

M3N.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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.14, A:G.98, A:L.99, A:Y.100, A:Y.100, A:R.228 Water bridges: A:R.228 M3N.5: 9 residues within 4Å: Chain B: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.14, B:G.98, B:L.99, B:Y.100, B:Y.100, B:R.228 Water bridges: B:R.228 M3N.11: 9 residues within 4Å: Chain C: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:Y.12, C:N.14, C:G.98, C:L.99, C:Y.100, C:Y.100, C:R.228 Water bridges: C:R.228 M3N.13: 9 residues within 4Å: Chain D: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.14, D:G.98, D:L.99, D:Y.100, D:Y.100, D:R.228 Water bridges: D:R.228

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 7 residues within 4Å: Chain A: S.113, L.115, N.124, L.126, V.179, H.180, A.189 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.180 Water bridges: B:D.139 EDO.8: 7 residues within 4Å: Chain B: S.113, K.114, L.115, N.124, L.126, V.179, H.180 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.180 Water bridges: B:A.125, B:P.178, A:D.139 EDO.12: 7 residues within 4Å: Chain C: S.113, L.115, N.124, L.126, V.179, H.180, A.189 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:H.180 Water bridges: D:D.139 EDO.16: 7 residues within 4Å: Chain D: S.113, K.114, L.115, N.124, L.126, V.179, H.180 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:H.180 Water bridges: D:A.125, D:P.178, C:D.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Francois-Heude, M. et al., Synthesis of High-Mannose Oligosaccharide Analogues through Click Chemistry: True Functional Mimics of Their Natural Counterparts Against Lectins?. Chemistry (2015)

Release Date

2014-12-17

Peptides

Concanavalin-A: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Concanavalin-A

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