SMTL ID : 7mg8.1

Concanavalin A bound to a DNA glycoconjugate, Man-CGCG

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-tetramer

Ligands

4 x DC- DG- DC- DG: DNA (5'-D(P*CP*GP*CP*G)-3')(Non-covalent)

DC-DG-DC-DG.1: 3 residues within 4Å: Chain A: S.21, P.23 Ligands: SQ0.9 Protein-ligand interaction information (PLIP) not available DC-DG-DC-DG.2: 2 residues within 4Å: Chain B: Y.100 Ligands: SQ0.10 Protein-ligand interaction information (PLIP) not available DC-DG-DC-DG.11: 3 residues within 4Å: Chain C: S.21, P.23 Ligands: SQ0.19 Protein-ligand interaction information (PLIP) not available DC-DG-DC-DG.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 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.8, B:D.10, B:D.19, B:H.24 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 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.8, D:D.10, D:D.19, D:H.24

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: D.10, Y.12, N.14, D.19, D.208 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.10, A:D.10, A:Y.12, A:D.19 CA.7: 5 residues within 4Å: Chain B: D.10, Y.12, N.14, D.19, D.208 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.10, B:D.10, B:Y.12, B:D.19 CA.14: 5 residues within 4Å: Chain C: D.10, Y.12, N.14, D.19, D.208 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.10, C:D.10, C:Y.12, C:D.19 CA.17: 5 residues within 4Å: Chain D: D.10, Y.12, N.14, D.19, D.208 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.10, D:D.10, D:Y.12, D:D.19

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

MAN.5: 11 residues within 4Å: Chain A: Y.12, N.14, T.97, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 Ligands: SQ0.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.99, A:Y.100, A:R.228 MAN.8: 11 residues within 4Å: Chain B: Y.12, N.14, T.97, 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:L.99, B:Y.100, B:Y.100, B:D.208, B:R.228 MAN.15: 11 residues within 4Å: Chain C: Y.12, N.14, T.97, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 Ligands: SQ0.19 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.14, C:L.99, C:Y.100, C:D.208, C:R.228 MAN.18: 11 residues within 4Å: Chain D: Y.12, N.14, T.97, 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:L.99, D:Y.100, D:Y.100, D:D.208, D:D.208, 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.13, S.21, Y.100 Ligands: DC-DG-DC-DG.1, MAN.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.13 Hydrogen bonds: A:Y.12, A:S.21, A:Y.100 SQ0.10: 7 residues within 4Å: Chain B: Y.12, P.13, T.15, Y.100, H.205 Ligands: DC-DG-DC-DG.2, MAN.8 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.12 Hydrogen bonds: B:Y.12, B:Y.12, B:T.15, B:H.205 SQ0.19: 6 residues within 4Å: Chain C: Y.12, P.13, S.21, Y.100 Ligands: DC-DG-DC-DG.11, MAN.15 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:P.13 Hydrogen bonds: C:Y.12, C:S.21 SQ0.20: 7 residues within 4Å: Chain D: Y.12, P.13, T.15, Y.100, H.205 Ligands: DC-DG-DC-DG.12, MAN.18 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:Y.12 Hydrogen bonds: D:Y.12, D:T.15, D:H.205

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

Related Entries With Identical Sequence