SMTL ID : 4lej.1

Crystal Structure of the Korean pine (Pinus koraiensis) vicilin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-trimer

Ligands

3 x CU: COPPER (II) ION(Non-covalent)

CU.1: 5 residues within 4Å: Chain A: Y.11, C.282, P.283, H.284, H.323 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.282, A:H.284, A:H.323 CU.4: 5 residues within 4Å: Chain B: Y.11, C.282, P.283, H.284, H.323 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.282, B:H.284, B:H.323 CU.7: 5 residues within 4Å: Chain C: Y.11, C.282, P.283, H.284, H.323 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.282, C:H.284, C:H.323

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 5 residues within 4Å: Chain A: S.267, A.269, E.327, W.339, R.349 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.267, A:S.267 Water bridges: A:R.349, A:R.349 Salt bridges: A:R.349 PO4.5: 5 residues within 4Å: Chain B: S.267, A.269, E.327, W.339, R.349 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.267, B:S.267 Water bridges: B:R.349, B:R.349 Salt bridges: B:R.349 PO4.8: 5 residues within 4Å: Chain C: S.267, A.269, E.327, W.339, R.349 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.267, C:S.267, C:Y.317 Water bridges: C:R.349, C:R.349 Salt bridges: C:R.349

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: I.29, T.51, H.64, I.66, Y.135 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.51, A:T.51, A:H.64, A:Y.135 Water bridges: A:R.21, A:Y.139 GOL.6: 5 residues within 4Å: Chain B: I.29, T.51, H.64, I.66, Y.135 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.51, B:H.64 Water bridges: B:R.21, B:Y.139 GOL.9: 5 residues within 4Å: Chain C: I.29, T.51, H.64, I.66, Y.135 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.51, C:T.51, C:H.64 Water bridges: C:R.21, C:Y.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jin, T. et al., Crystal Structure of Korean Pine ( Pinus koraiensis ) 7S Seed Storage Protein with Copper Ligands. J.Agric.Food Chem. (2014)

Release Date

2014-01-22

Peptides

Vicilin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Vicilin