SMTL ID : 7un2.1

Crystal structure of a lectin from Canavalia maritima seed (ConM) complexed with Indole-3-butyric acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 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.4, H2O.4 CA.6: 4 residues within 4Å: Chain B: D.10, Y.12, N.14, D.19 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.10, B:D.10, B:Y.12, B:D.19, H2O.10 CA.11: 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.17, H2O.17 CA.16: 4 residues within 4Å: Chain D: D.10, Y.12, N.14, D.19 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.10, D:D.10, D:Y.12, D:D.19, H2O.23

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

MN.2: 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.2 MN.7: 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.7, H2O.7 MN.12: 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.15, H2O.15 MN.17: 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.20, H2O.21

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.14, A:N.14, A:G.98, A:L.99, A:Y.100, A:Y.100 Water bridges: A:R.228 GOL.9: 9 residues within 4Å: Chain B: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.14, B:N.14, B:G.98, B:L.99, B:Y.100, B:Y.100 Water bridges: B:R.228 GOL.13: 9 residues within 4Å: Chain C: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.14, C:N.14, C:G.98, C:L.99, C:Y.100, C:Y.100 Water bridges: C:R.228 GOL.19: 9 residues within 4Å: Chain D: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.14, D:N.14, D:G.98, D:L.99, D:Y.100, D:Y.100 Water bridges: D:R.228

2 x 3IB: 3-INDOLEBUTYRIC ACID(Non-covalent)

3IB.4: 6 residues within 4Å: Chain A: T.49, S.108, S.110, N.131, T.194 Chain C: S.117 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.49, A:T.194 Hydrogen bonds: A:S.108, A:S.110, A:N.131 3IB.14: 6 residues within 4Å: Chain A: S.117 Chain C: T.49, S.108, S.110, N.131, T.194 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:T.49, C:T.194 Hydrogen bonds: C:S.108, C:S.110, C:N.131

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

CL.5: 2 residues within 4Å: Chain A: D.235, A.236 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain B: D.235, A.236 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain C: D.235, A.236 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain D: D.235, A.236 Ligand excluded by PLIP

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

DBB.8: 11 residues within 4Å: Chain A: V.129, F.130, Q.137, D.139 Chain B: W.88, S.113, N.124, A.125, L.126, V.179, H.180 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:N.124, B:H.180, A:Q.137, A:D.139, A:D.139 Water bridges: B:P.178 DBB.18: 11 residues within 4Å: Chain C: V.129, F.130, Q.137, D.139 Chain D: W.88, S.113, N.124, A.125, L.126, V.179, H.180 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:Q.137, C:D.139, D:N.124, D:H.180 Water bridges: D:P.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Sousa, J.P. et al., Structural analysis of Canavalia maritima lectin complexed with auxins. To Be Published

Release Date

2023-04-19

Peptides

ConM: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

ConM

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