SMTL ID : 8wmk.1

Structure of ConA/Man2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

homo-tetramer

Ligands

2 x WU0: 4-[3-(4-carboxyphenyl)phenyl]benzoic acid(Non-covalent)

WU0.1: 5 residues within 4Å: Chain A: Y.12, T.15, D.16 Ligands: ETA.2, ETA.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.16 Hydrogen bonds: A:Y.12 WU0.10: 5 residues within 4Å: Chain C: Y.12, T.15, D.16 Ligands: ETA.11, ETA.13 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:D.16

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

ETA.2: 4 residues within 4Å: Chain A: Y.12, L.99 Ligands: WU0.1, MAN.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.12 ETA.4: 2 residues within 4Å: Ligands: WU0.1, MAN.5 No protein-ligand interaction detected (PLIP) ETA.11: 4 residues within 4Å: Chain C: Y.12, L.99 Ligands: WU0.10, MAN.12 No protein-ligand interaction detected (PLIP) ETA.13: 2 residues within 4Å: Ligands: WU0.10, MAN.14 No protein-ligand interaction detected (PLIP)

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

MAN.3: 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.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.14, A:G.98, A:L.99, A:Y.100, A:Y.100, A:R.228 MAN.5: 1 residues within 4Å: Ligands: ETA.4 No protein-ligand interaction detected (PLIP) MAN.12: 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: ETA.11 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.14, C:G.98, C:L.99, C:Y.100, C:Y.100, C:R.228 MAN.14: 1 residues within 4Å: Ligands: ETA.13 No protein-ligand interaction detected (PLIP)

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

MN.6: 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.1 MN.8: 5 residues within 4Å: Chain B: E.8, D.10, D.19, H.24 Ligands: CA.9 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.2, H2O.3 MN.15: 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.4, H2O.4 MN.17: 5 residues within 4Å: Chain D: E.8, D.10, D.19, H.24 Ligands: CA.18 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.5, H2O.5

4 x CA: CALCIUM ION(Non-covalent)

CA.7: 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:D.19, H2O.1, H2O.1 CA.9: 5 residues within 4Å: Chain B: D.10, Y.12, N.14, D.19 Ligands: MN.8 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.10, B:D.10, B:D.19, H2O.2, H2O.3 CA.16: 4 residues within 4Å: Chain C: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.10, C:D.10, C:D.19, H2O.4, H2O.4 CA.18: 5 residues within 4Å: Chain D: D.10, Y.12, N.14, D.19 Ligands: MN.17 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.10, D:D.10, D:D.19, H2O.5, 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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Concanavalin-A

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