SMTL ID : 4q56.1

Structure of Helix aspersa agglutinin with natural glycosylation and N-acetyl-alpha-D-galactosamine (GalNAc)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

homo-hexamer

Ligands

6 x NAG- FUC- GAL- FUC- NAG- BMA: alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-alpha-L-fucopyranose-(1-3)-[beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)(Non-covalent)

NAG-FUC-GAL-FUC-NAG-BMA.1: 8 residues within 4Å: Chain A: K.18, V.19, P.20, E.31, A.33, N.35, K.78 Chain B: K.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.31, A:E.31, A:K.78, A:K.18 Water bridges: A:A.33 NAG-FUC-GAL-FUC-NAG-BMA.6: 8 residues within 4Å: Chain B: K.18, V.19, P.20, E.31, A.33, N.35, K.78 Chain C: K.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.31, B:E.31, B:K.78, B:K.18 Water bridges: B:A.33 NAG-FUC-GAL-FUC-NAG-BMA.11: 8 residues within 4Å: Chain A: K.7 Chain C: K.18, V.19, P.20, E.31, A.33, N.35, K.78 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.31, C:E.31, C:K.78, C:K.18 Water bridges: C:A.33 NAG-FUC-GAL-FUC-NAG-BMA.16: 8 residues within 4Å: Chain D: K.18, V.19, P.20, E.31, A.33, N.35, K.78 Chain E: K.7 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.31, D:K.78, D:K.18 Water bridges: D:A.33 NAG-FUC-GAL-FUC-NAG-BMA.21: 8 residues within 4Å: Chain E: K.18, V.19, P.20, E.31, A.33, N.35, K.78 Chain F: K.7 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.31, E:K.78, E:K.18 Water bridges: E:A.33 NAG-FUC-GAL-FUC-NAG-BMA.26: 8 residues within 4Å: Chain D: K.7 Chain F: K.18, V.19, P.20, E.31, A.33, N.35, K.78 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:E.31, F:K.78, F:K.18 Water bridges: F:A.33

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

ACT.2: 9 residues within 4Å: Chain A: N.62, R.64, H.85, N.86 Chain D: H.85 Ligands: A2G.3, ZN.5, ACT.17, ZN.20 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:N.86 Water bridges: A:R.64 Salt bridges: A:R.64, A:H.85, D:H.85 ACT.7: 9 residues within 4Å: Chain B: N.62, R.64, H.85, N.86 Chain F: H.85 Ligands: A2G.8, ZN.10, ACT.27, ZN.30 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:N.86 Water bridges: B:R.64 Salt bridges: B:R.64, B:H.85, F:H.85 ACT.12: 9 residues within 4Å: Chain C: N.62, R.64, H.85, N.86 Chain E: H.85 Ligands: A2G.13, ZN.15, ACT.22, ZN.25 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:N.86 Water bridges: C:R.64 Salt bridges: C:R.64, C:H.85, E:H.85 ACT.17: 9 residues within 4Å: Chain A: H.85 Chain D: N.62, R.64, H.85, N.86 Ligands: ACT.2, ZN.5, A2G.18, ZN.20 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:N.86 Water bridges: D:R.64 Salt bridges: D:R.64, D:H.85, A:H.85 ACT.22: 9 residues within 4Å: Chain C: H.85 Chain E: N.62, R.64, H.85, N.86 Ligands: ACT.12, ZN.15, A2G.23, ZN.25 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain E Salt bridges: C:H.85, E:R.64, E:H.85 Hydrogen bonds: E:N.86 Water bridges: E:R.64 ACT.27: 9 residues within 4Å: Chain B: H.85 Chain F: N.62, R.64, H.85, N.86 Ligands: ACT.7, ZN.10, A2G.28, ZN.30 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:N.86 Water bridges: F:R.64 Salt bridges: F:R.64, F:H.85, B:H.85

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

A2G.3: 8 residues within 4Å: Chain A: G.25, R.26, D.27, N.62, R.64, W.84, H.85 Ligands: ACT.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:D.27 Hydrogen bonds: A:G.25, A:D.27, A:D.27, A:N.62, A:R.64, A:W.84 Water bridges: A:G.25, A:R.26 Salt bridges: A:R.64, A:H.85 A2G.8: 8 residues within 4Å: Chain B: G.25, R.26, D.27, N.62, R.64, W.84, H.85 Ligands: ACT.7 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:D.27 Hydrogen bonds: B:G.25, B:D.27, B:D.27, B:N.62, B:R.64, B:W.84 Water bridges: B:G.25, B:R.26 Salt bridges: B:R.64, B:H.85 A2G.13: 8 residues within 4Å: Chain C: G.25, R.26, D.27, N.62, R.64, W.84, H.85 Ligands: ACT.12 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:D.27 Hydrogen bonds: C:G.25, C:D.27, C:D.27, C:N.62, C:R.64, C:W.84 Water bridges: C:G.25, C:R.26 Salt bridges: C:R.64, C:H.85 A2G.18: 8 residues within 4Å: Chain D: G.25, R.26, D.27, N.62, R.64, W.84, H.85 Ligands: ACT.17 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:D.27 Hydrogen bonds: D:G.25, D:D.27, D:N.62, D:R.64, D:W.84 Water bridges: D:G.25, D:R.26 Salt bridges: D:R.64, D:H.85 A2G.23: 8 residues within 4Å: Chain E: G.25, R.26, D.27, N.62, R.64, W.84, H.85 Ligands: ACT.22 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:D.27 Hydrogen bonds: E:G.25, E:D.27, E:N.62, E:R.64, E:W.84 Water bridges: E:G.25, E:R.26 Salt bridges: E:R.64, E:H.85 A2G.28: 8 residues within 4Å: Chain F: G.25, R.26, D.27, N.62, R.64, W.84, H.85 Ligands: ACT.27 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:D.27 Hydrogen bonds: F:G.25, F:D.27, F:N.62, F:R.64, F:W.84 Water bridges: F:G.25, F:R.26 Salt bridges: F:R.64, F:H.85

6 x NA: SODIUM ION(Post Translational Modification)(Non-covalent)

NA.4: 1 residues within 4Å: Chain A: Q.59 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.59 Water bridges: A:Q.59 NA.9: 1 residues within 4Å: Chain B: Q.59 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.59 Water bridges: B:Q.59 NA.14: 1 residues within 4Å: Chain C: Q.59 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.59 Water bridges: C:Q.59 NA.19: 1 residues within 4Å: Chain D: Q.59 1 PLIP interactions: 1 interactions with chain D Water bridges: D:Q.59 NA.24: 1 residues within 4Å: Chain E: Q.59 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Q.59 Water bridges: E:Q.59 NA.29: 1 residues within 4Å: Chain F: Q.59 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Q.59 Water bridges: F:Q.59

6 x ZN: ZINC ION(Non-functional Binders)(Non-covalent)

ZN.5: 5 residues within 4Å: Chain A: H.85 Chain D: H.85 Ligands: ACT.2, ACT.17, ZN.20 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: D:H.85, A:H.85, ACT.2, ACT.17 ZN.10: 5 residues within 4Å: Chain B: H.85 Chain F: H.85 Ligands: ACT.7, ACT.27, ZN.30 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain F, 1 Ligand-Ligand interactions Metal complexes: B:H.85, F:H.85, ACT.7 ZN.15: 5 residues within 4Å: Chain C: H.85 Chain E: H.85 Ligands: ACT.12, ACT.22, ZN.25 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain E, 1 Ligand-Ligand interactions Metal complexes: C:H.85, E:H.85, ACT.12 ZN.20: 5 residues within 4Å: Chain A: H.85 Chain D: H.85 Ligands: ACT.2, ZN.5, ACT.17 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Metal complexes: D:H.85, A:H.85 ZN.25: 5 residues within 4Å: Chain C: H.85 Chain E: H.85 Ligands: ACT.12, ZN.15, ACT.22 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain E, 1 Ligand-Ligand interactions Metal complexes: C:H.85, E:H.85, ACT.22 ZN.30: 5 residues within 4Å: Chain B: H.85 Chain F: H.85 Ligands: ACT.7, ZN.10, ACT.27 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: F:H.85, B:H.85, ACT.27

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Pietrzyk, A.J. et al., Structural studies of Helix aspersa agglutinin complexed with GalNAc: A lectin that serves as a diagnostic tool. Int.J.Biol.Macromol. (2015)

Release Date

2015-10-14

Peptides

Helix aspersa agglutinin (HAA): ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Helix aspersa agglutinin (HAA)