SMTL ID : 2ccv.1

Structure of Helix Pomatia agglutinin with zinc and N-acetyl-alpha-D- galactoseamine (GalNAc)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-hexamer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 2 residues within 4Å: Chain A: H.84 Ligands: ACT.4 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.84, ACT.4 ZN.6: 2 residues within 4Å: Chain B: H.84 Ligands: ACT.9 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.84, ACT.9 ZN.11: 2 residues within 4Å: Chain C: H.84 Ligands: ACT.14 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:H.84, ACT.14 ZN.16: 2 residues within 4Å: Chain D: H.84 Ligands: ACT.19 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:H.84, ACT.19 ZN.21: 2 residues within 4Å: Chain E: H.84 Ligands: ACT.24 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Ligand interactions Metal complexes: E:H.84, ACT.24 ZN.26: 2 residues within 4Å: Chain F: H.84 Ligands: ACT.29 2 PLIP interactions: 1 interactions with chain F, 1 Ligand-Ligand interactions Metal complexes: F:H.84, ACT.29

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

A2G.2: 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: ACT.4 10 PLIP interactions: 1 interactions with chain C, 9 interactions with chain A Hydrogen bonds: C:D.55, A:G.24, A:D.26, A:D.26, A:N.61, A:R.63, A:W.83 Water bridges: A:G.24 Salt bridges: A:R.63, A:H.84 A2G.7: 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: ACT.9 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.24, B:D.26, B:D.26, B:N.61, B:R.63, B:W.83, A:D.55 Water bridges: B:G.24 Salt bridges: B:R.63, B:H.84 A2G.12: 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: ACT.14 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:G.24, C:D.26, C:D.26, C:N.61, C:R.63, C:W.83, B:D.55 Water bridges: C:G.24 Salt bridges: C:R.63, C:H.84 A2G.17: 10 residues within 4Å: Chain D: G.24, R.25, D.26, N.61, R.63, W.83, H.84 Chain E: D.55, Y.89 Ligands: ACT.19 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:G.24, D:D.26, D:N.61, D:R.63, D:W.83, E:D.55 Water bridges: D:G.24 Salt bridges: D:R.63, D:H.84 A2G.22: 10 residues within 4Å: Chain E: G.24, R.25, D.26, N.61, R.63, W.83, H.84 Chain F: D.55, Y.89 Ligands: ACT.24 9 PLIP interactions: 8 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:G.24, E:D.26, E:N.61, E:R.63, E:W.83, F:D.55 Water bridges: E:G.24 Salt bridges: E:R.63, E:H.84 A2G.27: 10 residues within 4Å: Chain D: D.55, Y.89 Chain F: G.24, R.25, D.26, N.61, R.63, W.83, H.84 Ligands: ACT.29 9 PLIP interactions: 8 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:G.24, F:D.26, F:N.61, F:R.63, F:W.83, D:D.55 Water bridges: F:G.24 Salt bridges: F:R.63, F:H.84

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: S.59, Q.60, N.61, R.63, N.85 Chain C: Q.58 Ligands: ACT.4 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.61, A:R.63, A:R.63, A:N.85, C:Q.58 GOL.8: 7 residues within 4Å: Chain A: Q.58 Chain B: S.59, Q.60, N.61, R.63, N.85 Ligands: ACT.9 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.61, B:R.63, B:R.63, B:N.85, A:Q.58 GOL.13: 7 residues within 4Å: Chain B: Q.58 Chain C: S.59, Q.60, N.61, R.63, N.85 Ligands: ACT.14 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:Q.58, C:N.61, C:R.63, C:R.63, C:N.85 GOL.18: 7 residues within 4Å: Chain D: S.59, Q.60, N.61, R.63, N.85 Chain E: Q.58 Ligands: ACT.19 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:N.61, D:R.63, D:R.63, D:N.85, E:Q.58 GOL.23: 7 residues within 4Å: Chain E: S.59, Q.60, N.61, R.63, N.85 Chain F: Q.58 Ligands: ACT.24 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:N.61, E:R.63, E:R.63, E:N.85, F:Q.58 GOL.28: 7 residues within 4Å: Chain D: Q.58 Chain F: S.59, Q.60, N.61, R.63, N.85 Ligands: ACT.29 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:N.61, F:R.63, F:R.63, F:N.85, D:Q.58

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

ACT.4: 7 residues within 4Å: Chain A: N.61, R.63, H.84, N.85 Ligands: ZN.1, A2G.2, GOL.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.85 Salt bridges: A:R.63, A:H.84 ACT.9: 7 residues within 4Å: Chain B: N.61, R.63, H.84, N.85 Ligands: ZN.6, A2G.7, GOL.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.85 Salt bridges: B:R.63, B:H.84 ACT.14: 7 residues within 4Å: Chain C: N.61, R.63, H.84, N.85 Ligands: ZN.11, A2G.12, GOL.13 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.85 Salt bridges: C:R.63, C:H.84 ACT.19: 7 residues within 4Å: Chain D: N.61, R.63, H.84, N.85 Ligands: ZN.16, A2G.17, GOL.18 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.85 Salt bridges: D:R.63, D:H.84 ACT.24: 7 residues within 4Å: Chain E: N.61, R.63, H.84, N.85 Ligands: ZN.21, A2G.22, GOL.23 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.85 Salt bridges: E:R.63, E:H.84 ACT.29: 7 residues within 4Å: Chain F: N.61, R.63, H.84, N.85 Ligands: ZN.26, A2G.27, GOL.28 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:N.85 Salt bridges: F:R.63, F:H.84

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

NAG.5: 3 residues within 4Å: Chain A: N.34, S.70, K.77 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.34, A:S.70 NAG.10: 3 residues within 4Å: Chain B: N.34, S.70, K.77 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.34, B:S.70 NAG.15: 3 residues within 4Å: Chain C: N.34, S.70, K.77 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.34, C:S.70 NAG.20: 3 residues within 4Å: Chain D: N.34, S.70, K.77 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.34, D:S.70 NAG.25: 3 residues within 4Å: Chain E: N.34, S.70, K.77 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.34, E:S.70 NAG.30: 3 residues within 4Å: Chain F: N.34, S.70, K.77 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.34, F:S.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sanchez, J.-F. et al., Biochemical and Structural Analysis of Helix Pomatia Agglutinin. A Hexameric Lectin with a Novel Fold. J.Biol.Chem. (2006)

Release Date

2006-05-15

Peptides

HELIX POMATIA AGGLUTININ: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

HELIX POMATIA AGGLUTININ