SMTL ID : 8wmg.1

Structure of ConA/Man3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-dimer

Ligands

1 x WRW: 4-[3,5-bis(4-carboxyphenyl)phenyl]benzoic acid(Non-covalent)

WRW.1: 6 residues within 4Å: Chain A: Y.12, T.15, D.16 Ligands: ETA.2, ETA.4, ETA.6 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.16

3 x ETA: ETHANOLAMINE(Non-covalent)(Non-functional Binders)

ETA.2: 3 residues within 4Å: Chain A: T.15 Ligands: WRW.1, MAN.3 No protein-ligand interaction detected (PLIP) ETA.4: 2 residues within 4Å: Ligands: WRW.1, MAN.5 No protein-ligand interaction detected (PLIP) ETA.6: 4 residues within 4Å: Chain A: Y.12, L.99 Ligands: WRW.1, MAN.7 No protein-ligand interaction detected (PLIP)

3 x MAN: alpha-D-mannopyranose(Non-covalent)(Non-functional Binders)

MAN.3: 5 residues within 4Å: Chain A: D.19, P.20, S.21, Y.22 Ligands: ETA.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.21, A:S.21 MAN.5: 1 residues within 4Å: Ligands: ETA.4 No protein-ligand interaction detected (PLIP) MAN.7: 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: ETA.6 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

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

MN.8: 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.2 MN.10: 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.4, H2O.4

2 x CA: CALCIUM ION(Non-covalent)

CA.9: 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:D.10, A:Y.12, H2O.1, H2O.1 CA.11: 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:D.10, B:D.19, H2O.4, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, L. et al., Rational design of inducing ligands with three-dimensional supramolecular interactions to build protein crystalline frameworks. To Be Published

Release Date

2023-12-06

Peptides

Concanavalin-A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Concanavalin-A

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