SMTL ID : 7mg9.1

Concanavalin A bound to DNA glycoconjugates, Man-TTTT and Man-AAAA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-tetramer

Ligands

2 x DA- DA- DA- DA: DNA (5'-D(P*AP*AP*AP*A)-3')(Non-covalent)

DA-DA-DA-DA.1: 2 residues within 4Å: Chain A: P.23 Ligands: SQ0.9 Protein-ligand interaction information (PLIP) not available DA-DA-DA-DA.11: 2 residues within 4Å: Chain C: P.23 Ligands: SQ0.19 Protein-ligand interaction information (PLIP) not available

2 x DT- DT- DT- DT: DNA (5'-D(P*TP*TP*TP*T)-3')(Non-covalent)

DT-DT-DT-DT.2: 2 residues within 4Å: Chain B: Y.100 Ligands: SQ0.10 Protein-ligand interaction information (PLIP) not available DT-DT-DT-DT.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 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.8, A:D.10, A:D.19, A:H.24 MN.6: 4 residues within 4Å: Chain B: E.8, D.10, D.19, H.24 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.8, B:D.10, B:D.19, B:H.24, H2O.4 MN.13: 4 residues within 4Å: Chain C: E.8, D.10, D.19, H.24 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.8, C:D.10, C:D.19, C:H.24 MN.16: 4 residues within 4Å: Chain D: E.8, D.10, D.19, H.24 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.8, D:D.10, D:D.19, D:H.24, H2O.9

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: D.10, Y.12, N.14, D.19 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.10, A:D.10, A:Y.12, A:D.19 CA.7: 4 residues within 4Å: Chain B: D.10, Y.12, N.14, D.19 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.10, B:D.10, B:Y.12, B:D.19, H2O.4 CA.14: 4 residues within 4Å: Chain C: D.10, Y.12, N.14, D.19 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.10, C:D.10, C:Y.12, C:D.19 CA.17: 4 residues within 4Å: Chain D: D.10, Y.12, N.14, D.19 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.10, D:D.10, D:Y.12, D:D.19, H2O.10

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 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.14, B:G.98, B:L.99, B:Y.100, B:Y.100, 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 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: 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 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

4 x SQ0: 3-{[2-(2-hydroxyethoxy)ethyl]amino}-4-[(6-hydroxyhexyl)amino]cyclobut-3-ene-1,2-dione(Non-covalent)

SQ0.9: 5 residues within 4Å: Chain A: Y.12, P.13, Y.100 Ligands: DA-DA-DA-DA.1, MAN.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.12 SQ0.10: 5 residues within 4Å: Chain B: Y.12, P.13, T.15 Ligands: DT-DT-DT-DT.2, MAN.8 No protein-ligand interaction detected (PLIP) SQ0.19: 5 residues within 4Å: Chain C: Y.12, P.13, Y.100 Ligands: DA-DA-DA-DA.11, MAN.15 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.12, C:Y.100 SQ0.20: 5 residues within 4Å: Chain D: Y.12, P.13, T.15 Ligands: DT-DT-DT-DT.12, MAN.18 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.12

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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