SMTL ID : 6v7j.1

The C2221 crystal form of canavalin at 173 K

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

3 x BEZ: BENZOIC ACID(Non-covalent)

BEZ.1: 10 residues within 4Å: Chain A: N.284, L.286, F.294, H.297, N.299, V.304, L.306, I.348, L.356, R.376 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.286, A:L.306, A:L.306, A:I.348, A:L.356 Hydrogen bonds: A:N.284, A:N.299 Salt bridges: A:H.297, A:R.376 pi-Stacking: A:F.294 BEZ.5: 9 residues within 4Å: Chain B: N.284, L.286, F.294, H.297, N.299, V.304, L.306, I.348, R.376 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.286, B:L.306, B:L.306, B:I.348 Hydrogen bonds: B:N.284, B:N.299 Salt bridges: B:H.297, B:R.376 pi-Stacking: B:F.294 BEZ.7: 10 residues within 4Å: Chain C: N.284, L.286, F.294, H.297, N.299, V.304, L.306, I.348, L.356, R.376 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:L.286, C:L.306, C:L.306, C:I.348, C:L.356 Hydrogen bonds: C:N.284, C:N.299 Salt bridges: C:H.297, C:R.376 pi-Stacking: C:F.294

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: N.260, N.261, G.263, K.264, Q.287, M.288, N.289 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.260, A:Q.287, A:N.289, A:N.289 GOL.6: 8 residues within 4Å: Chain B: N.260, N.261, Y.262, G.263, K.264, Q.287, M.288, N.289 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.260, B:Q.287 GOL.8: 8 residues within 4Å: Chain C: N.260, N.261, Y.262, G.263, K.264, Q.287, M.288, N.289 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.262, C:K.264, C:K.264, C:N.289

3 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: D.396, F.399, P.400, G.401 Chain C: E.214 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.396, A:F.399, A:G.401 CA.4: 6 residues within 4Å: Chain A: A.308, N.309, E.310, G.311, N.363, M.364 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.310, A:N.363 CA.9: 7 residues within 4Å: Chain C: G.115, Q.116, N.150, D.152, Q.155, N.156, L.157 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:Q.155

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McPherson, A., Binding of benzoic acid and anions within the cupin domains of the vicilin protein canavalin from jack bean (Canavalia ensiformis): Crystal structures. Biochem.Biophys.Res.Commun. (2020)

Release Date

2020-02-19

Peptides

Canavalin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Canavalin

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