SMTL ID : 6flz.1

Structure of AcmJRL, a mannose binding jacalin related lectin from Ananas comosus, in complex with methyl-mannose.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-tetramer

Ligands

6 x MMA: methyl alpha-D-mannopyranoside(Non-covalent)

MMA.1: 8 residues within 4Å: Chain A: A.34, H.35, A.36, D.38, G.60, G.61, L.84, L.133 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.34, A:H.35, A:A.36, A:G.61 Water bridges: A:G.60 Salt bridges: A:H.35 MMA.2: 9 residues within 4Å: Chain A: E.13, G.14, V.87, L.90, F.130, G.131, S.132, L.133, D.135 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.14, A:G.131, A:S.132, A:L.133, A:D.135, A:D.135 MMA.4: 9 residues within 4Å: Chain B: E.13, G.14, V.87, L.90, F.130, G.131, S.132, L.133, D.135 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.14, B:G.131, B:S.132, B:L.133, B:D.135, B:D.135 Water bridges: B:E.13 MMA.7: 8 residues within 4Å: Chain C: A.34, H.35, A.36, D.38, G.60, G.61, L.84, L.133 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:A.34, C:H.35, C:A.36, C:G.61 Water bridges: C:G.60 Salt bridges: C:H.35 MMA.8: 9 residues within 4Å: Chain C: E.13, G.14, V.87, L.90, F.130, G.131, S.132, L.133, D.135 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.14, C:G.131, C:S.132, C:L.133, C:D.135, C:D.135 MMA.10: 9 residues within 4Å: Chain D: E.13, G.14, V.87, L.90, F.130, G.131, S.132, L.133, D.135 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:G.14, D:G.131, D:S.132, D:L.133, D:D.135, D:D.135 Water bridges: D:E.13

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

CIT.3: 5 residues within 4Å: Chain A: H.35, L.84, R.92, L.108, H.110 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.110 Water bridges: A:R.92 Salt bridges: A:H.35, A:R.92, A:R.92, A:H.110, A:H.110 CIT.5: 8 residues within 4Å: Chain B: D.18, I.19, D.20, Y.44, F.51, A.52, A.53, W.56 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.44, B:F.51 Hydrogen bonds: B:D.20, B:D.20, B:Y.44, B:Y.44 Water bridges: B:G.54 CIT.6: 5 residues within 4Å: Chain B: H.35, L.84, R.92, L.108, H.110 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.92 Salt bridges: B:H.35, B:R.92, B:R.92, B:H.110 CIT.9: 5 residues within 4Å: Chain C: H.35, L.84, R.92, L.108, H.110 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:H.110 Water bridges: C:R.92 Salt bridges: C:H.35, C:R.92, C:R.92, C:H.110, C:H.110 CIT.11: 8 residues within 4Å: Chain D: D.18, I.19, D.20, Y.44, F.51, A.52, A.53, W.56 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:Y.44, D:F.51 Hydrogen bonds: D:D.20, D:D.20, D:Y.44, D:Y.44 Water bridges: D:G.54 CIT.12: 5 residues within 4Å: Chain D: H.35, L.84, R.92, L.108, H.110 5 PLIP interactions: 5 interactions with chain D Water bridges: D:R.92 Salt bridges: D:H.35, D:R.92, D:R.92, D:H.110

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Azarkan, M. et al., Biochemical and structural characterization of a mannose binding jacalin-related lectin with two-sugar binding sites from pineapple (Ananas comosus) stem. Sci Rep (2018)

Release Date

2018-08-15

Peptides

Jacalin-like lectin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Jacalin-like lectin

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