SMTL ID : 4h55.1

Crystal structure of Canavalia brasiliensis seed lectin (ConBr) in complex with beta-d-ribofuranose

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.3, H2O.4 CA.5: 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.7 CA.9: 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.9, H2O.10 CA.13: 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.12, H2O.13

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.3, H2O.4 MN.6: 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.10: 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.10, H2O.10 MN.14: 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.13, H2O.13

4 x BDR: beta-D-ribofuranose(Non-covalent)

BDR.3: 8 residues within 4Å: Chain A: Y.12, N.14, T.97, G.98, L.99, Y.100, A.207, D.208 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.14, A:G.98, A:L.99, A:Y.100, A:D.208 BDR.7: 8 residues within 4Å: Chain B: Y.12, N.14, T.97, G.98, L.99, Y.100, A.207, D.208 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.14, B:G.98, B:L.99, B:Y.100, B:D.208 BDR.11: 8 residues within 4Å: Chain C: Y.12, N.14, T.97, G.98, L.99, Y.100, A.207, D.208 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.14, C:N.14, C:G.98, C:L.99, C:Y.100, C:D.208 BDR.15: 8 residues within 4Å: Chain D: Y.12, N.14, T.97, G.98, L.99, Y.100, A.207, D.208 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.14, D:N.14, D:G.98, D:L.99, D:Y.100, D:D.208

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

DBB.4: 9 residues within 4Å: Chain A: S.113, L.115, N.124, A.125, L.126, V.179, H.180 Chain D: F.130, D.139 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:N.124, D:F.130 Hydrogen bonds: A:S.113, A:L.115, A:N.124, A:L.126, A:H.180, D:D.139 DBB.8: 9 residues within 4Å: Chain B: S.113, L.115, N.124, A.125, L.126, V.179, H.180 Chain C: F.130, D.139 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:N.124, C:F.130 Hydrogen bonds: B:S.113, B:L.115, B:N.124, B:L.126, B:H.180, C:D.139 DBB.12: 9 residues within 4Å: Chain B: F.130, D.139 Chain C: S.113, L.115, N.124, A.125, L.126, V.179, H.180 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:N.124, B:F.130 Hydrogen bonds: C:S.113, C:L.115, C:N.124, C:L.126, C:H.180 DBB.16: 9 residues within 4Å: Chain A: F.130, D.139 Chain D: S.113, L.115, N.124, A.125, L.126, V.179, H.180 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain D Hydrophobic interactions: A:F.130, D:N.124 Hydrogen bonds: D:S.113, D:L.115, D:N.124, D:L.126, D:H.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Salviano, E. et al., Crystal structure of Canavalia brasiliensis seed lectin (ConBr) in complex with beta-d-ribofuranose. TO BE PUBLISHED

Release Date

2012-10-31

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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