SMTL ID : 1dgl.1

LECTIN FROM DIOCLEA GRANDIFLORA COMPLEXED TO TRIMANNOSIDE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x MMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]methyl alpha-D-mannopyranoside

MMA-MAN-MAN.1: 12 residues within 4Å: Chain A: Y.12, P.13, N.14, T.15, D.16, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.14, A:G.98, A:L.99, A:Y.100, A:Y.100, A:R.228, A:Y.12, A:D.16 Water bridges: A:T.97, A:N.168, A:G.227, A:R.228, A:Y.12, A:R.228 MMA-MAN-MAN.2: 12 residues within 4Å: Chain B: Y.12, P.13, N.14, T.15, D.16, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.14, B:G.98, B:L.99, B:Y.100, B:Y.100, B:R.228, B:Y.12, B:Y.12, B:D.16 Water bridges: B:N.168, B:G.226, B:R.228, B:N.14, B:N.14, B:R.228 MMA-MAN-MAN.7: 12 residues within 4Å: Chain C: Y.12, P.13, N.14, T.15, D.16, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.14, C:G.98, C:L.99, C:Y.100, C:Y.100, C:R.228, C:Y.12, C:Y.12, C:D.16 Water bridges: C:T.97, C:N.168, C:G.227, C:R.228, C:Y.100, C:R.228 MMA-MAN-MAN.8: 12 residues within 4Å: Chain D: Y.12, P.13, N.14, T.15, D.16, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.14, D:G.98, D:L.99, D:Y.100, D:Y.100, D:R.228, D:Y.12, D:D.16 Water bridges: D:N.168, D:G.226, D:R.228, D:Y.12, D:N.14, D:N.14, D:R.228

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: N.10, Y.12, N.14, D.19 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Y.12, A:D.19, H2O.1, H2O.1 CA.5: 4 residues within 4Å: Chain B: N.10, Y.12, N.14, D.19 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:Y.12, B:D.19, H2O.4, H2O.4 CA.9: 4 residues within 4Å: Chain C: N.10, Y.12, N.14, D.19 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:Y.12, C:D.19, H2O.8, H2O.8 CA.11: 4 residues within 4Å: Chain D: N.10, Y.12, N.14, D.19 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:Y.12, D:D.19, H2O.12, H2O.12

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

MN.4: 5 residues within 4Å: Chain A: E.8, N.10, D.19, H.24, S.34 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.8, A:D.19, A:H.24, H2O.1, H2O.1 MN.6: 4 residues within 4Å: Chain B: E.8, N.10, D.19, H.24 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.8, B:D.19, B:H.24, H2O.4, H2O.4 MN.10: 5 residues within 4Å: Chain C: E.8, N.10, D.19, H.24, S.34 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.8, C:D.19, C:H.24, H2O.8, H2O.8 MN.12: 4 residues within 4Å: Chain D: E.8, N.10, D.19, H.24 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.8, D:D.19, D:H.24, H2O.12, H2O.12

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Rozwarski, D.A. et al., Crystal structure of the lectin from Dioclea grandiflora complexed with core trimannoside of asparagine-linked carbohydrates. J.Biol.Chem. (1998)

Release Date

1999-06-01

Peptides

LECTIN: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

LECTIN