SMTL ID : 7mg7.1

Concanavalin A bound to a DNA glycoconjugate, Man-GTAC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

4 x DG- DT- DA- DC: DNA (5'-D(P*GP*TP*AP*C)-3')(Non-covalent)

DG-DT-DA-DC.1: 3 residues within 4Å: Chain A: P.23, H.205 Ligands: SQ0.9 Protein-ligand interaction information (PLIP) not available DG-DT-DA-DC.2: 2 residues within 4Å: Chain B: Y.100 Ligands: SQ0.10 Protein-ligand interaction information (PLIP) not available DG-DT-DA-DC.11: 3 residues within 4Å: Chain C: P.23, H.205 Ligands: SQ0.19 Protein-ligand interaction information (PLIP) not available DG-DT-DA-DC.12: 2 residues within 4Å: Chain D: Y.100 Ligands: SQ0.20 Protein-ligand interaction information (PLIP) not available

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

MN.3: 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.3 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.9, H2O.10 MN.13: 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.16, H2O.18 MN.16: 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.24, H2O.25

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 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.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.10, H2O.12 CA.14: 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.16 CA.17: 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.25, H2O.27

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

MAN.5: 10 residues within 4Å: Chain A: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 Ligands: SQ0.9 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 MAN.8: 10 residues within 4Å: Chain B: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 Ligands: SQ0.10 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 MAN.15: 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: SQ0.19 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.18: 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: SQ0.20 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 SQ0: 3-{[2-(2-hydroxyethoxy)ethyl]amino}-4-[(6-hydroxyhexyl)amino]cyclobut-3-ene-1,2-dione(Non-covalent)

SQ0.9: 6 residues within 4Å: Chain A: Y.12, P.23, Y.100, H.205 Ligands: DG-DT-DA-DC.1, MAN.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.12, A:Y.100 Water bridges: A:Y.12, A:P.13, A:N.14 SQ0.10: 9 residues within 4Å: Chain B: Y.12, P.13, N.14, T.15, D.16, L.99, Y.100 Ligands: DG-DT-DA-DC.2, MAN.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.12, B:T.15, B:D.16 Water bridges: B:N.14 SQ0.19: 6 residues within 4Å: Chain C: Y.12, P.23, Y.100, H.205 Ligands: DG-DT-DA-DC.11, MAN.15 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.12 Water bridges: C:Y.12, C:P.13, C:N.14 SQ0.20: 9 residues within 4Å: Chain D: Y.12, P.13, N.14, T.15, D.16, L.99, Y.100 Ligands: DG-DT-DA-DC.12, MAN.18 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.15 Water bridges: D:N.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Partridge, B.E. et al., Redefining Protein Interfaces within Protein Single Crystals with DNA. J.Am.Chem.Soc. (2021)

Release Date

2021-06-16

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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