SMTL ID : 4pcr.2 (1 other biounit)

Crystal structure of Canavalia brasiliensis seed lectin (ConBr) complexed with Gamma-Aminobutyric Acid (GABA)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 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.2, H2O.2 CA.7: 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.4, H2O.4 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.6, H2O.6 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.8, H2O.8

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.8: 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.4 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.5, H2O.6 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.7, H2O.8

4 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.3: 7 residues within 4Å: Chain A: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.207 Hydrogen bonds: A:N.14, A:D.208 IPA.9: 8 residues within 4Å: Chain B: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, R.228 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.99, B:A.207 Hydrogen bonds: B:N.14, B:D.208 IPA.17: 7 residues within 4Å: Chain C: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:A.207 Hydrogen bonds: C:N.14, C:D.208 IPA.23: 8 residues within 4Å: Chain D: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, R.228 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.99, D:A.207 Hydrogen bonds: D:N.14, D:D.208

6 x ABU: GAMMA-AMINO-BUTANOIC ACID(Non-covalent)

ABU.4: 9 residues within 4Å: Chain A: S.113, K.114, L.115, N.124, A.125, L.126, V.179, H.180 Chain B: D.139 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.126 Hydrogen bonds: A:S.113, A:H.180, B:D.139 Water bridges: A:H.180 ABU.5: 5 residues within 4Å: Chain A: L.115, N.124, E.183 Chain B: Q.132, F.133 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Q.132 Hydrogen bonds: B:F.133, A:N.124 Water bridges: A:H.180 ABU.10: 4 residues within 4Å: Chain A: Q.132, F.133 Chain B: N.124, E.183 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:E.183, A:Q.132 Hydrogen bonds: B:E.183, A:F.133 Water bridges: B:N.124, A:Q.137 ABU.18: 9 residues within 4Å: Chain C: S.113, K.114, L.115, N.124, A.125, L.126, V.179, H.180 Chain D: D.139 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.126 Hydrogen bonds: C:S.113, C:H.180 Water bridges: D:Q.137 ABU.19: 5 residues within 4Å: Chain C: L.115, N.124, E.183 Chain D: Q.132, F.133 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Q.132 Hydrogen bonds: D:F.133, C:N.124 ABU.24: 4 residues within 4Å: Chain C: Q.132, F.133 Chain D: N.124, E.183 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:Q.132, D:E.183 Hydrogen bonds: C:F.133, D:E.183 Water bridges: C:Q.137, D:N.124

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

PEG.6: 3 residues within 4Å: Chain A: T.49, T.194 Chain C: S.119 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:S.119, C:T.123, A:T.49 PEG.13: 3 residues within 4Å: Chain B: K.46, V.47, P.68 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.47 PEG.14: 5 residues within 4Å: Chain B: L.107, N.131, Q.132, G.152, N.153 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.152 PEG.20: 3 residues within 4Å: Chain A: S.119 Chain C: T.49, T.194 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.119, A:T.123 PEG.27: 3 residues within 4Å: Chain D: K.46, V.47, P.68 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:V.47 PEG.28: 5 residues within 4Å: Chain D: L.107, N.131, Q.132, G.152, N.153 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.152

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.11: 1 residues within 4Å: Chain B: S.161 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.161 EDO.12: 3 residues within 4Å: Chain B: K.35, K.36, T.37 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.37, B:T.37 EDO.25: 1 residues within 4Å: Chain D: S.161 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.161 EDO.26: 3 residues within 4Å: Chain D: K.35, K.36, T.37 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.37, D:T.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Delatorre, P. et al., Crystal structure of Canavalia brasiliensis seed lectin (ConBr) complexed with Gamma-Aminobutyric Acid (GABA). To Be Published

Release Date

2015-04-22

Peptides

Concanavalin-Br: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
A

D
D

Concanavalin-Br

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