SMTL ID : 1jw6.1 (1 other biounit)

Crystal Structure of the Complex of Concanavalin A and Hexapeptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-tetramer

Ligands

4 x MET- TYR- TRP- TYR- PRO- TYR: PROTEIN (6-MER)(Non-covalent)

MET-TYR-TRP-TYR-PRO-TYR.1: 13 residues within 4Å: Chain A: T.11, Y.12, P.13, T.15, G.18, D.19, P.20, S.21, Y.22, P.23, H.205, P.206 Ligands: PTD.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.20, A:Y.22, A:P.23 Hydrogen bonds: A:S.21, A:S.21, A:S.21, A:P.206 Water bridges: A:Y.22 MET-TYR-TRP-TYR-PRO-TYR.6: 13 residues within 4Å: Chain B: T.11, Y.12, P.13, T.15, G.18, D.19, P.20, S.21, Y.22, P.23, H.205, P.206 Ligands: PTD.9 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:P.20, B:Y.22, B:P.23 Hydrogen bonds: B:S.21, B:S.21, B:S.21, B:P.206 Water bridges: B:Y.22 MET-TYR-TRP-TYR-PRO-TYR.11: 13 residues within 4Å: Chain C: T.11, Y.12, P.13, T.15, G.18, D.19, P.20, S.21, Y.22, P.23, H.205, P.206 Ligands: PTD.14 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:P.20, C:Y.22, C:P.23 Hydrogen bonds: C:S.21, C:S.21, C:S.21, C:Y.22 Water bridges: C:Y.22 MET-TYR-TRP-TYR-PRO-TYR.16: 13 residues within 4Å: Chain D: T.11, Y.12, P.13, T.15, G.18, D.19, P.20, S.21, Y.22, P.23, H.205, P.206 Ligands: PTD.19 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:P.20, D:Y.22, D:P.23 Hydrogen bonds: D:S.21, D:S.21, D:S.21, D:Y.22 Water bridges: D:Y.22

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

MN.2: 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.2, H2O.2 MN.7: 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.6, H2O.6 MN.12: 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.9, H2O.9 MN.17: 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.13, H2O.13

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 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:Y.12, A:D.19, H2O.2, H2O.2 CA.8: 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.5, H2O.6 CA.13: 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:Y.12, C:D.19, H2O.9, H2O.10 CA.18: 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.13, H2O.13

4 x PTD: PENTANEDIAL(Non-covalent)

PTD.4: 4 residues within 4Å: Chain A: Y.22, K.39 Ligands: MET-TYR-TRP-TYR-PRO-TYR.1, MET-TYR-TRP-TYR-PRO-TYR.1 No protein-ligand interaction detected (PLIP) PTD.9: 4 residues within 4Å: Chain B: Y.22, K.39 Ligands: MET-TYR-TRP-TYR-PRO-TYR.6, MET-TYR-TRP-TYR-PRO-TYR.6 No protein-ligand interaction detected (PLIP) PTD.14: 4 residues within 4Å: Chain C: Y.22, K.39 Ligands: MET-TYR-TRP-TYR-PRO-TYR.11, MET-TYR-TRP-TYR-PRO-TYR.11 No protein-ligand interaction detected (PLIP) PTD.19: 4 residues within 4Å: Chain D: Y.22, K.39 Ligands: MET-TYR-TRP-TYR-PRO-TYR.16, MET-TYR-TRP-TYR-PRO-TYR.16 No protein-ligand interaction detected (PLIP)

4 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.5: 2 residues within 4Å: Chain A: P.86, E.87 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.86 Hydrogen bonds: A:E.87, A:E.87 IPA.10: 2 residues within 4Å: Chain B: P.86, E.87 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.86 Hydrogen bonds: B:E.87, B:E.87 IPA.15: 2 residues within 4Å: Chain C: P.86, E.87 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:P.86 Hydrogen bonds: C:E.87, C:E.87, C:E.87 IPA.20: 2 residues within 4Å: Chain D: P.86, E.87 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:P.86 Hydrogen bonds: D:E.87, D:E.87, D:E.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Z. et al., Crystal structure of the complex of concanavalin A and hexapeptide. J.Protein Chem. (2001)

Release Date

2001-09-26

Peptides

Concanavalin A: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Concanavalin A

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