SMTL ID : 2eaa.1

Crystal Structure of Adzuki Bean 7S Globulin-3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-trimer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: E.382, F.385, P.386, A.387 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.382, A:F.385, A:P.386, H2O.4, H2O.15 CA.4: 4 residues within 4Å: Chain B: E.382, F.385, P.386, A.387 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.382, B:F.385, B:P.386, B:A.387, H2O.5 CA.7: 4 residues within 4Å: Chain C: E.382, F.385, P.386, A.387 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.382, C:F.385, C:P.386, C:A.387

3 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 5 residues within 4Å: Chain A: R.46, Q.49, N.142, H.144, R.145 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.49, A:N.142, A:H.144 Salt bridges: A:R.46, A:H.144, A:H.144, A:R.145 CIT.5: 6 residues within 4Å: Chain B: R.46, Q.49, N.142, H.144, R.145 Chain C: K.52 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.49, B:N.142 Salt bridges: B:R.46, B:H.144, B:H.144, B:H.144, B:R.145 CIT.8: 7 residues within 4Å: Chain A: K.52, Q.55 Chain C: R.46, Q.49, N.142, H.144, R.145 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:N.142 Water bridges: C:R.46, C:D.48 Salt bridges: C:R.46, C:H.144, C:H.144, C:H.144, C:R.145

3 x ACY: ACETIC ACID(Non-functional Binders)

ACY.3: 7 residues within 4Å: Chain A: W.249, H.281, N.283, V.288, I.334, V.340, R.362 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.249, A:V.288, A:I.334 Hydrogen bonds: A:N.283, A:N.283 Salt bridges: A:H.281, A:R.362 ACY.6: 6 residues within 4Å: Chain B: W.249, H.281, N.283, V.288, I.334, R.362 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.249, B:V.288 Hydrogen bonds: B:N.283 Salt bridges: B:H.281 ACY.9: 7 residues within 4Å: Chain C: W.249, H.281, N.283, V.288, I.334, F.350, R.362 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:V.288, C:I.334, C:F.350 Hydrogen bonds: C:N.283 Salt bridges: C:H.281, C:R.362

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fukuda, T. et al., Characterization and crystallography of recombinant 7S globulins of Adzuki bean and structure-function relationships with 7S globulins of various crops. J.Agric.Food Chem. (2008)

Release Date

2008-02-05

Peptides

7S globulin-3: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

7S globulin-3