SMTL ID : 6vb8.1

Crystal structure of a lectin from Canavalia brasiliensis seed (ConBr) complexed with indole-3-acetic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, R.228 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.14, A:N.14, A:G.98, A:L.99, A:Y.100, A:Y.100 GOL.8: 8 residues within 4Å: Chain B: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, R.228 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.14, B:N.14, B:G.98, B:L.99, B:Y.100, B:Y.100 GOL.15: 8 residues within 4Å: Chain C: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, R.228 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.14, C:N.14, C:G.98, C:L.99, C:Y.100, C:Y.100 GOL.22: 8 residues within 4Å: Chain D: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, R.228 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.14, D:N.14, D:G.98, D:L.99, D:Y.100, D:Y.100

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 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.9: 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.3, H2O.3 CA.16: 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.4, H2O.5 CA.23: 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.6, H2O.7

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

MN.3: 4 residues within 4Å: Chain A: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.8, A:D.10, A:D.19, A:H.24, H2O.1, H2O.1 MN.10: 4 residues within 4Å: Chain B: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.8, B:D.10, B:D.19, B:H.24, H2O.3, H2O.3 MN.17: 4 residues within 4Å: Chain C: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.8, C:D.10, C:D.19, C:H.24, H2O.4, H2O.5 MN.24: 4 residues within 4Å: Chain D: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.8, D:D.10, D:D.19, D:H.24, H2O.6, H2O.6

8 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 3 residues within 4Å: Chain A: R.228, D.235, A.236 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: N.14, D.16, R.228 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: R.228, D.235, A.236 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: N.14, D.16, R.228 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain C: R.228, D.235, A.236 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain C: N.14, D.16, R.228 Ligand excluded by PLIP CL.25: 3 residues within 4Å: Chain D: R.228, D.235, A.236 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain D: N.14, D.16, R.228 Ligand excluded by PLIP

4 x DBB: D-ALPHA-AMINOBUTYRIC ACID(Non-covalent)

DBB.6: 11 residues within 4Å: Chain A: W.88, S.113, N.124, A.125, L.126, V.179, H.180 Chain D: M.129, F.130, Q.137, D.139 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:A.125, A:A.125, A:H.180, D:Q.137, D:D.139, D:D.139 Water bridges: A:N.124, A:N.124 DBB.13: 11 residues within 4Å: Chain B: W.88, S.113, N.124, A.125, L.126, V.179, H.180 Chain C: M.129, F.130, Q.137, D.139 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:Q.137, C:D.139, C:D.139, B:A.125, B:A.125, B:H.180 Water bridges: B:N.124, B:N.124 DBB.20: 11 residues within 4Å: Chain B: M.129, F.130, Q.137, D.139 Chain C: W.88, S.113, N.124, A.125, L.126, V.179, H.180 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:A.125, C:A.125, C:H.180, B:Q.137, B:D.139 Water bridges: C:N.124, C:N.124 DBB.27: 11 residues within 4Å: Chain A: M.129, F.130, Q.137, D.139 Chain D: W.88, S.113, N.124, A.125, L.126, V.179, H.180 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain D Hydrogen bonds: A:Q.137, A:D.139, D:A.125, D:A.125, D:H.180 Water bridges: D:N.124, D:N.124

4 x IAC: 1H-INDOL-3-YLACETIC ACID(Non-covalent)

IAC.7: 6 residues within 4Å: Chain A: T.49, S.108, N.131, T.196 Chain C: S.117, N.118 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.49, A:T.196 Hydrogen bonds: A:S.108 IAC.14: 6 residues within 4Å: Chain B: T.49, S.108, N.131, T.196 Chain D: S.117, N.118 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.49, B:T.196 Hydrogen bonds: B:S.108 IAC.21: 6 residues within 4Å: Chain A: S.117, N.118 Chain C: T.49, S.108, N.131, T.196 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:T.49, C:T.196 Hydrogen bonds: C:S.108 IAC.28: 6 residues within 4Å: Chain B: S.117, N.118 Chain D: T.49, S.108, N.131, T.196 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:T.49, D:T.196 Hydrogen bonds: D:S.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bezerra, E.H.S. et al., Structural insights into phytohormone interaction to plant lectin ConBr. To Be Published

Release Date

2020-12-23

Peptides

Concanavalin-Br: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Concanavalin-Br

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