SMTL ID : 2fmd.1

Structural basis of carbohydrate recognition by Bowringia milbraedii seed agglutinin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

4 x MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose(Non-covalent)

MAN-MAN.1: 9 residues within 4Å: Chain A: A.85, D.86, G.105, R.106, Y.131, N.133, G.217, Q.218, Y.219 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.106, A:N.133, A:G.217, A:Q.218, A:Y.219, A:Y.219 Water bridges: A:G.104 MAN-MAN.4: 9 residues within 4Å: Chain B: A.85, D.86, G.105, R.106, Y.131, N.133, G.217, Q.218, Y.219 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.106, B:N.133, B:G.217, B:Q.218, B:Y.219, B:Y.219 Water bridges: B:G.104 MAN-MAN.7: 9 residues within 4Å: Chain C: A.85, D.86, G.105, R.106, Y.131, N.133, G.217, Q.218, Y.219 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.106, C:N.133, C:G.217, C:Q.218, C:Y.219, C:Y.219 Water bridges: C:G.104 MAN-MAN.10: 9 residues within 4Å: Chain D: A.85, D.86, G.105, R.106, Y.131, N.133, G.217, Q.218, Y.219 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.106, D:N.133, D:G.217, D:Q.218, D:Y.219, D:Y.219 Water bridges: D:G.104

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.129, Y.131, N.133, D.138 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.129, A:D.129, A:D.138, H2O.5, H2O.5 CA.5: 4 residues within 4Å: Chain B: D.129, Y.131, N.133, D.138 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.129, B:D.129, B:D.138, H2O.13, H2O.13 CA.8: 4 residues within 4Å: Chain C: D.129, Y.131, N.133, D.138 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.129, C:D.129, C:D.138, H2O.22, H2O.22 CA.11: 4 residues within 4Å: Chain D: D.129, Y.131, N.133, D.138 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.129, D:D.129, D:D.138, H2O.30, H2O.30

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

MN.3: 4 residues within 4Å: Chain A: E.127, D.129, D.138, H.143 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.127, A:D.129, A:D.138, A:H.143, H2O.5, H2O.5 MN.6: 4 residues within 4Å: Chain B: E.127, D.129, D.138, H.143 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.127, B:D.129, B:D.138, B:H.143, H2O.13, H2O.13 MN.9: 4 residues within 4Å: Chain C: E.127, D.129, D.138, H.143 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.127, C:D.129, C:D.138, C:H.143, H2O.22, H2O.22 MN.12: 4 residues within 4Å: Chain D: E.127, D.129, D.138, H.143 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.127, D:D.129, D:D.138, D:H.143, H2O.30, H2O.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Buts, L. et al., Structural basis of carbohydrate recognition by a Man(alpha1-2)Man-specific lectin from Bowringia milbraedii. Glycobiology (2006)

Release Date

2006-08-22

Peptides

Lectin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Lectin