SMTL ID : 2ofd.2 (1 other biounit)

The Crystal Structure of Sclerotium rolfsii lectin in complex with N-acetyl-D-galactosamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-tetramer

Ligands

6 x NGA: 2-acetamido-2-deoxy-beta-D-galactopyranose(Non-covalent)

NGA.1: 7 residues within 4Å: Chain A: Y.28, S.48, G.49, H.71, N.72, Y.97, R.106 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.49, A:N.72, A:N.72, A:R.106, A:R.106 Water bridges: A:S.48, A:N.72, A:N.72, A:Y.97 Salt bridges: A:H.71 NGA.3: 8 residues within 4Å: Chain B: Y.28, S.48, G.49, H.71, N.72, Y.73, Y.97, R.106 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.48, B:G.49, B:N.72, B:R.106 Water bridges: B:Y.28, B:H.71, B:N.72, B:Y.97, B:Y.97, B:R.106 Salt bridges: B:H.71 NGA.4: 8 residues within 4Å: Chain B: D.78, I.79, V.80, T.81, R.102, Y.113, V.115, K.116 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.115 Hydrogen bonds: B:I.79, B:T.81, B:R.102 Water bridges: B:N.101 Salt bridges: B:R.102 NGA.7: 7 residues within 4Å: Chain C: Y.28, S.48, G.49, H.71, N.72, Y.97, R.106 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:G.49, C:N.72, C:N.72, C:R.106, C:R.106 Water bridges: C:Y.28, C:S.48, C:H.71, C:N.72, C:N.72, C:Y.97 Salt bridges: C:H.71 NGA.9: 8 residues within 4Å: Chain D: Y.28, S.48, G.49, H.71, N.72, Y.73, Y.97, R.106 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:S.48, D:G.49, D:N.72, D:R.106 Water bridges: D:N.72, D:Y.97, D:Y.97, D:R.106 Salt bridges: D:H.71 NGA.10: 8 residues within 4Å: Chain D: D.78, I.79, V.80, T.81, R.102, Y.113, V.115, K.116 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:V.115 Hydrogen bonds: D:I.79, D:T.81, D:R.102, D:Y.113 Water bridges: D:N.101 Salt bridges: D:R.102

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 4 residues within 4Å: Chain A: D.78, I.79, R.108, Y.113 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.113 ACT.5: 4 residues within 4Å: Chain B: N.13, N.15, K.119, R.121 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.13, B:N.15 Salt bridges: B:R.121 ACT.6: 3 residues within 4Å: Chain B: S.98, K.100, E.103 No protein-ligand interaction detected (PLIP) ACT.8: 4 residues within 4Å: Chain C: D.78, I.79, R.108, Y.113 No protein-ligand interaction detected (PLIP) ACT.11: 4 residues within 4Å: Chain D: N.13, N.15, K.119, R.121 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.13, D:N.15 Salt bridges: D:R.121 ACT.12: 3 residues within 4Å: Chain D: S.98, K.100, E.103 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leonidas, D.D. et al., Structural Basis for the Carbohydrate Recognition of the Sclerotium rolfsii Lectin. J.Mol.Biol. (2007)

Release Date

2007-05-01

Peptides

Sclerotium rolfsii lectin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Sclerotium rolfsii lectin

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