SMTL ID : 5zac.1

Crystal structure of ConA-R2M

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

homo-tetramer

Ligands

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

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

6 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.10, Y.12, N.14, D.19 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.10, A:D.10, A:Y.12, A:D.19, H2O.1 CA.3: 3 residues within 4Å: Chain A: E.122 Chain B: T.49, P.68 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.122 CA.5: 4 residues within 4Å: Chain B: D.10, Y.12, N.14, D.19 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.10, B:Y.12, B:D.19, H2O.3 CA.7: 4 residues within 4Å: Chain C: D.10, Y.12, N.14, D.19 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.10, C:D.10, C:Y.12, C:D.19, H2O.6 CA.11: 5 residues within 4Å: Chain D: D.10, Y.12, N.14, D.19 Ligands: MN.10 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.8 CA.12: 3 residues within 4Å: Chain C: K.116 Chain D: T.49, P.68 No protein-ligand interaction detected (PLIP)

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

MAN.8: 10 residues within 4Å: Chain C: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 Ligands: TA5.9 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.14, C:G.98, C:L.99, C:Y.100, C:Y.100, C:R.228 Water bridges: C:R.228 MAN.13: 10 residues within 4Å: Chain D: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 Ligands: TA5.14 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.14, D:G.98, D:L.99, D:Y.100, D:Y.100, D:R.228

2 x TA5: 2H-1,2,3-TRIAZOL-4-YLMETHANOL(Non-covalent)

TA5.9: 2 residues within 4Å: Chain C: L.99 Ligands: MAN.8 No protein-ligand interaction detected (PLIP) TA5.14: 2 residues within 4Å: Chain D: Y.12 Ligands: MAN.13 No protein-ligand interaction detected (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
C

D
D

Concanavalin-A

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