SMTL ID : 2cgz.1

Structure of Helix Pomatia agglutinin with Tn antigen

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-hexamer

Ligands

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 1 residues within 4Å: Chain A: N.34 No protein-ligand interaction detected (PLIP) NAG.4: 1 residues within 4Å: Chain B: N.34 No protein-ligand interaction detected (PLIP) NAG.7: 1 residues within 4Å: Chain C: N.34 No protein-ligand interaction detected (PLIP) NAG.10: 1 residues within 4Å: Chain D: N.34 No protein-ligand interaction detected (PLIP) NAG.13: 1 residues within 4Å: Chain E: N.34 No protein-ligand interaction detected (PLIP) NAG.16: 1 residues within 4Å: Chain F: N.34 No protein-ligand interaction detected (PLIP)

6 x SER: SERINE(Non-covalent)

SER.2: 2 residues within 4Å: Chain A: H.84 Ligands: A2G.3 No protein-ligand interaction detected (PLIP) SER.5: 2 residues within 4Å: Chain B: H.84 Ligands: A2G.6 No protein-ligand interaction detected (PLIP) SER.8: 2 residues within 4Å: Chain C: H.84 Ligands: A2G.9 No protein-ligand interaction detected (PLIP) SER.11: 2 residues within 4Å: Chain D: H.84 Ligands: A2G.12 No protein-ligand interaction detected (PLIP) SER.14: 2 residues within 4Å: Chain E: H.84 Ligands: A2G.15 No protein-ligand interaction detected (PLIP) SER.17: 2 residues within 4Å: Chain F: H.84 Ligands: A2G.18 No protein-ligand interaction detected (PLIP)

6 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Non-covalent)

A2G.3: 10 residues within 4Å: Chain A: G.24, R.25, D.26, N.61, R.63, W.83, H.84 Chain C: D.55, Y.89 Ligands: SER.2 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:D.26 Hydrogen bonds: A:G.24, A:D.26, A:N.61, A:R.63, A:W.83, C:D.55 A2G.6: 10 residues within 4Å: Chain A: D.55, Y.89 Chain B: G.24, R.25, D.26, N.61, R.63, W.83, H.84 Ligands: SER.5 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:D.26 Hydrogen bonds: B:G.24, B:D.26, B:N.61, B:R.63, B:W.83, A:D.55 A2G.9: 10 residues within 4Å: Chain B: D.55, Y.89 Chain C: G.24, R.25, D.26, N.61, R.63, W.83, H.84 Ligands: SER.8 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:D.55, C:G.24, C:D.26, C:N.61, C:R.63, C:W.83 Hydrophobic interactions: C:D.26 A2G.12: 10 residues within 4Å: Chain D: G.24, R.25, D.26, N.61, R.63, W.83, H.84 Chain F: D.55, Y.89 Ligands: SER.11 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: D:D.26 Hydrogen bonds: D:G.24, D:D.26, D:D.26, D:N.61, D:R.63, D:W.83, D:H.84, F:D.55 A2G.15: 10 residues within 4Å: Chain D: D.55, Y.89 Chain E: G.24, R.25, D.26, N.61, R.63, W.83, H.84 Ligands: SER.14 9 PLIP interactions: 8 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:D.26 Hydrogen bonds: E:G.24, E:D.26, E:D.26, E:N.61, E:R.63, E:W.83, E:H.84, D:D.55 A2G.18: 10 residues within 4Å: Chain E: D.55, Y.89 Chain F: G.24, R.25, D.26, N.61, R.63, W.83, H.84 Ligands: SER.17 9 PLIP interactions: 8 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:D.26 Hydrogen bonds: F:G.24, F:D.26, F:D.26, F:N.61, F:R.63, F:W.83, F:H.84, E:D.55

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Lescar, J. et al., Structural Basis for Recognition of Breast and Colon Cancer Epitopes Tn Antigen and Forssman Disaccharide by Helix Pomatia Lectin. Glycobiology (2007)

Release Date

2007-05-01

Peptides

AGGLUTININ: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

AGGLUTININ

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