SMTL ID : 3ju9.1

Crystal structure of a lectin from Canavalia brasiliensis seed (ConBr) complexed with alpha-aminobutyric acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

DBB.1: 11 residues within 4Å: Chain A: W.88, S.113, L.115, N.124, A.125, L.126, V.179, H.180 Chain D: M.129, F.130, D.139 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:L.115 Hydrogen bonds: A:N.124, A:A.125, A:H.180, D:Q.137, D:D.139, D:D.139 DBB.7: 11 residues within 4Å: Chain B: W.88, S.113, L.115, N.124, A.125, L.126, V.179, H.180 Chain C: M.129, F.130, D.139 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:L.115 Hydrogen bonds: B:N.124, B:A.125, B:H.180, C:Q.137, C:D.139, C:D.139 DBB.13: 11 residues within 4Å: Chain B: M.129, F.130, D.139 Chain C: W.88, S.113, L.115, N.124, A.125, L.126, V.179, H.180 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.115 Hydrogen bonds: C:N.124, C:A.125, C:H.180, B:Q.137, B:D.139 DBB.19: 11 residues within 4Å: Chain A: M.129, F.130, D.139 Chain D: W.88, S.113, L.115, N.124, A.125, L.126, V.179, H.180 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:L.115 Hydrogen bonds: D:N.124, D:A.125, D:H.180, A:Q.137, A:D.139

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 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:L.99, A:Y.100, A:Y.100 Water bridges: A:T.226, A:R.228 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:L.99, B:Y.100, B:Y.100 Water bridges: B:T.226, B:R.228 GOL.14: 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:L.99, C:Y.100, C:Y.100 Water bridges: C:T.226, C:R.228 GOL.20: 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:L.99, D:Y.100, D:Y.100 Water bridges: D:T.226, D:R.228

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 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.1 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.6, H2O.6 CA.15: 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.11, H2O.11 CA.21: 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.17, H2O.17

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

MN.4: 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.6, H2O.6 MN.16: 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.11, H2O.12 MN.22: 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.17, H2O.17

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

CL.5: 3 residues within 4Å: Chain A: R.228, D.235, A.236 Ligand excluded by PLIP CL.6: 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.17: 3 residues within 4Å: Chain C: R.228, D.235, A.236 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain C: N.14, D.16, R.228 Ligand excluded by PLIP CL.23: 3 residues within 4Å: Chain D: R.228, D.235, A.236 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain D: N.14, D.16, R.228 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bezerra, E.H. et al., Structural analysis of ConBr reveals molecular correlation between the carbohydrate recognition domain and endothelial NO synthase activation. Biochem.Biophys.Res.Commun. (2011)

Release Date

2010-12-08

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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