SMTL ID : 7uod.1

Crystal structure of a lectin from Canavalia maritima seed (ConM) complexed with 2,4-dichloro-phenoxyacetic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

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

DBB.1: 12 residues within 4Å: Chain A: W.88, S.113, L.115, N.124, A.125, L.126, V.179, H.180 Chain B: V.129, F.130, Q.137, D.139 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.115 Hydrogen bonds: A:N.124, A:H.180, B:D.139, B:D.139 Water bridges: A:P.178, B:D.139 DBB.8: 12 residues within 4Å: Chain A: V.129, F.130, Q.137, D.139 Chain B: W.88, S.113, L.115, N.124, A.125, L.126, V.179, H.180 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.115 Hydrogen bonds: B:N.124, B:A.125, B:H.180, A:Q.137, A:D.139 DBB.16: 12 residues within 4Å: Chain C: W.88, S.113, L.115, N.124, A.125, L.126, V.179, H.180 Chain D: V.129, F.130, Q.137, D.139 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.115 Hydrogen bonds: C:N.124, C:H.180, D:D.139 Water bridges: C:P.178, D:D.139 DBB.23: 12 residues within 4Å: Chain C: V.129, F.130, Q.137, D.139 Chain D: W.88, S.113, L.115, N.124, A.125, L.126, V.179, H.180 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:L.115 Hydrogen bonds: D:N.124, D:A.125, D:H.180, C:Q.137, C:D.139, C:D.139

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.2, H2O.4 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.10, H2O.10 CA.17: 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.14, H2O.16 CA.24: 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.22, H2O.22

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.2 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.8, H2O.8 MN.18: 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.13, H2O.14 MN.25: 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.20

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: 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:G.98, A:L.99, A:Y.100, A:Y.100 Water bridges: A:R.228 GOL.11: 9 residues within 4Å: Chain B: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.14, B:N.14, B:L.99, B:Y.100, B:Y.100 GOL.19: 7 residues within 4Å: Chain C: N.14, G.98, L.99, Y.100, A.207, D.208, 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.26: 9 residues within 4Å: Chain D: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.14, D:N.14, D:L.99, D:Y.100, D:Y.100

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 7 residues within 4Å: Chain A: N.124, E.183, S.185 Chain B: Q.132, F.133, S.134, G.152 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.185, A:S.185 PEG.13: 6 residues within 4Å: Chain A: Q.132, F.133, S.134 Chain B: N.124, E.183, S.185 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.185 Water bridges: B:E.183 PEG.20: 7 residues within 4Å: Chain C: N.124, E.183, S.185 Chain D: Q.132, F.133, S.134, G.152 2 PLIP interactions: 2 interactions with chain C Water bridges: C:S.185, C:S.185 PEG.28: 6 residues within 4Å: Chain C: Q.132, F.133, S.134 Chain D: N.124, E.183, S.185 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.185

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

CL.6: 2 residues within 4Å: Chain A: D.235, A.236 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: N.14, D.16, R.228 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain B: D.235, A.236 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain B: N.14, D.16 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain C: D.235, A.236 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain C: N.14, D.16, R.228 Ligand excluded by PLIP CL.29: 2 residues within 4Å: Chain D: D.235, A.236 Ligand excluded by PLIP CL.30: 2 residues within 4Å: Chain D: N.14, D.16 Ligand excluded by PLIP

2 x CFA: (2,4-DICHLOROPHENOXY)ACETIC ACID(Non-covalent)

CFA.12: 6 residues within 4Å: Chain B: T.49, S.108, S.110, N.131, T.194 Chain D: S.117 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:T.49, B:T.194 Hydrogen bonds: B:N.131 Water bridges: B:S.108, B:S.108 CFA.27: 6 residues within 4Å: Chain B: S.117 Chain D: T.49, S.108, S.110, N.131, T.194 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:T.49, D:T.194 Hydrogen bonds: D:N.131 Water bridges: D:S.108, D:S.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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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