SMTL ID : 5z5y.2 (1 other biounit)

Crystal structure of ConA-R4M

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-tetramer

Ligands

4 x 2KO: 2-{2-[2-(2-{4-[(alpha-D-mannopyranosyloxy)methyl]-1H-1,2,3-triazol-1-yl}ethoxy)ethoxy]ethoxy}ethyl 2-[3,6-bis(diethylamino)-9H-xanthen-9-yl]benzoate(Non-covalent)

2KO.1: 10 residues within 4Å: Chain A: Y.12, N.14, D.16, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.99, A:Y.100, A:Y.100 Hydrogen bonds: A:N.14, A:G.98, A:L.99, A:Y.100, A:Y.100, A:D.208, A:R.228 Water bridges: A:R.228 2KO.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 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.99 Hydrogen bonds: B:Y.12, B:N.14, B:G.98, B:L.99, B:Y.100, B:Y.100, B:D.208, B:R.228 2KO.8: 10 residues within 4Å: Chain C: Y.12, N.14, D.16, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:L.99, C:Y.100, C:Y.100 Hydrogen bonds: C:N.14, C:G.98, C:L.99, C:Y.100, C:Y.100, C:D.208, C:R.228 Water bridges: C:R.228 2KO.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 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:L.99 Hydrogen bonds: D:Y.12, D:N.14, D:G.98, D:L.99, D:Y.100, D:Y.100, D:D.208, D:R.228

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

MN.2: 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.1, H2O.1 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.3, H2O.3 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.4, H2O.4 MN.13: 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.6, H2O.7

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 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.1, H2O.2 CA.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.3, H2O.4 CA.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:Y.12, C:D.19, H2O.4, H2O.5 CA.14: 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.7, H2O.7

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

CL.4: 2 residues within 4Å: Chain A: R.90 Chain B: Y.176 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain C: R.90 Chain D: Y.176 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, R.T. et al., Competition between Supramolecular Interaction and Protein-Protein Interaction in Protein Crystallization:Effects of Crystallization Method and Small Molecular Bridge. Ind Eng Chem Res (2018)

Release Date

2018-05-30

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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