SMTL ID : 4pcr.1 (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-dimer

Ligands

2 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

2 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

2 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

3 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 A, 2 interactions with chain B Hydrogen bonds: A:N.124, B:F.133 Water bridges: A:H.180 Hydrophobic interactions: B:Q.132 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 A, 3 interactions with chain B Hydrophobic interactions: A:Q.132, B:E.183 Hydrogen bonds: A:F.133, B:E.183 Water bridges: A:Q.137, B:N.124

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

PEG.6: 2 residues within 4Å: Chain A: T.49, T.194 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: 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

2 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

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Concanavalin-Br

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