SMTL ID : 1hqw.1

CRYSTAL STRUCTURE OF THE COMPLEX OF CONCANAVALIN A WITH A TRIPEPTIDE YPY

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x TYR- PRO- TYR: YPY(Non-covalent)

TYR-PRO-TYR.1: 4 residues within 4Å: Chain A: T.15, D.16, S.21 Ligands: PTD.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.15, A:S.21 Water bridges: A:T.15, A:D.16 TYR-PRO-TYR.5: 4 residues within 4Å: Chain B: T.15, D.16, S.21 Ligands: PTD.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.15, B:S.21 Water bridges: B:T.15, B:D.16 TYR-PRO-TYR.9: 4 residues within 4Å: Chain C: T.15, D.16, S.21 Ligands: PTD.12 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.15, C:S.21 TYR-PRO-TYR.13: 4 residues within 4Å: Chain D: T.15, D.16, S.21 Ligands: PTD.16 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.15, D:S.21

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

MN.2: 5 residues within 4Å: Chain A: E.8, D.10, D.19, H.24, S.34 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.8, A:D.10, A:D.19, A:H.24, H2O.1 MN.6: 5 residues within 4Å: Chain B: E.8, D.10, D.19, H.24, S.34 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.6 MN.10: 5 residues within 4Å: Chain C: E.8, D.10, D.19, H.24, S.34 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.8, C:D.10, C:D.19, C:H.24, H2O.10 MN.14: 5 residues within 4Å: Chain D: E.8, D.10, D.19, H.24, S.34 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.15

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.1, H2O.2 CA.7: 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.6, H2O.7 CA.11: 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.10, H2O.11 CA.15: 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.15, H2O.16

4 x PTD: PENTANEDIAL(Non-covalent)

PTD.4: 3 residues within 4Å: Chain A: Y.22, K.39 Ligands: TYR-PRO-TYR.1 No protein-ligand interaction detected (PLIP) PTD.8: 3 residues within 4Å: Chain B: Y.22, K.39 Ligands: TYR-PRO-TYR.5 No protein-ligand interaction detected (PLIP) PTD.12: 3 residues within 4Å: Chain C: Y.22, K.39 Ligands: TYR-PRO-TYR.9 No protein-ligand interaction detected (PLIP) PTD.16: 3 residues within 4Å: Chain D: Y.22, K.39 Ligands: TYR-PRO-TYR.13 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Z. et al., Crystal structure of the complex of concanavalin A and tripeptide. J.PROTEIN CHEM. (2001)

Release Date

2003-10-07

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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