SMTL ID : 8jeb.1

Crystal structure of CGL1 from Crassostrea gigas, mannotetraose-bound form (CGL1/Man(alpha)1-2Man(alpha)1-2Man(alpha)1-6Man)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-hexamer

Ligands

6 x MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose(Non-covalent)

MAN-MAN.1: 7 residues within 4Å: Chain A: F.54, A.55, G.56, K.113, H.115, Y.122, E.129 No protein-ligand interaction detected (PLIP) MAN-MAN.3: 9 residues within 4Å: Chain B: S.35, E.37, F.54, A.55, G.56, K.113, H.115, Y.122, E.129 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.35, B:E.37 MAN-MAN.15: 7 residues within 4Å: Chain C: F.54, A.55, G.56, K.113, H.115, Y.122, E.129 No protein-ligand interaction detected (PLIP) MAN-MAN.17: 9 residues within 4Å: Chain D: S.35, E.37, F.54, A.55, G.56, K.113, H.115, Y.122, E.129 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.35, D:E.37 MAN-MAN.29: 9 residues within 4Å: Chain B: Y.105 Chain E: F.54, A.55, G.56, K.113, H.115, Y.122, E.129 Ligands: MAN-MAN.18 No protein-ligand interaction detected (PLIP) MAN-MAN.31: 9 residues within 4Å: Chain F: S.35, E.37, F.54, A.55, G.56, K.113, H.115, Y.122, E.129 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.35

6 x MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose(Non-covalent)

MAN-MAN.2: 9 residues within 4Å: Chain A: D.21, I.22, K.42, H.46, H.51, E.58, I.60, F.125, A.126 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.21, A:K.42, A:E.58, A:A.126 MAN-MAN.4: 9 residues within 4Å: Chain B: D.21, I.22, K.42, H.46, H.51, E.58, I.60, F.125, A.126 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.21, B:K.42, B:E.58, B:A.126 MAN-MAN.16: 9 residues within 4Å: Chain C: D.21, I.22, K.42, H.46, H.51, E.58, I.60, F.125, A.126 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.21, C:K.42, C:E.58, C:A.126 MAN-MAN.18: 12 residues within 4Å: Chain D: D.21, I.22, K.42, H.46, H.51, E.58, I.60, F.125, A.126 Chain E: F.118 Ligands: MAN-MAN.29, MAN-MAN.29 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.21, D:K.42, D:E.58, D:A.126 MAN-MAN.30: 9 residues within 4Å: Chain E: D.21, I.22, K.42, H.46, H.51, E.58, I.60, F.125, A.126 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:D.21, E:K.42, E:E.58, E:A.126 MAN-MAN.32: 9 residues within 4Å: Chain F: D.21, I.22, K.42, H.46, H.51, E.58, I.60, F.125, A.126 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:D.21, F:K.42, F:E.58, F:A.126

15 x ACY: ACETIC ACID(Non-functional Binders)

ACY.5: 2 residues within 4Å: Chain A: W.3, I.92 No protein-ligand interaction detected (PLIP) ACY.6: 4 residues within 4Å: Chain A: S.5, N.63, Y.64, E.65 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.64 Water bridges: A:Y.64 ACY.10: 3 residues within 4Å: Chain B: S.5, Y.64, E.65 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.64 ACY.11: 3 residues within 4Å: Chain B: W.3, L.67, I.92 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.67, B:I.92 Hydrogen bonds: B:W.3 ACY.12: 7 residues within 4Å: Chain B: Q.81, R.102, V.103, L.104, L.109, Y.135, E.136 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.109, B:E.136 Hydrogen bonds: B:Q.81, B:L.104 ACY.19: 2 residues within 4Å: Chain C: W.3, I.92 No protein-ligand interaction detected (PLIP) ACY.20: 4 residues within 4Å: Chain C: S.5, N.63, Y.64, E.65 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.64 Water bridges: C:Y.64 ACY.24: 3 residues within 4Å: Chain D: S.5, Y.64, E.65 1 PLIP interactions: 1 interactions with chain D Water bridges: D:Y.64 ACY.25: 3 residues within 4Å: Chain D: W.3, L.67, I.92 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.67, D:I.92 Hydrogen bonds: D:W.3 ACY.26: 7 residues within 4Å: Chain D: Q.81, R.102, V.103, L.104, L.109, Y.135, E.136 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.109, D:E.136 Hydrogen bonds: D:Q.81, D:L.104 ACY.33: 2 residues within 4Å: Chain E: W.3, I.92 No protein-ligand interaction detected (PLIP) ACY.34: 4 residues within 4Å: Chain E: S.5, N.63, Y.64, E.65 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Y.64 Water bridges: E:Y.64 ACY.38: 3 residues within 4Å: Chain F: S.5, Y.64, E.65 1 PLIP interactions: 1 interactions with chain F Water bridges: F:Y.64 ACY.39: 3 residues within 4Å: Chain F: W.3, L.67, I.92 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:L.67, F:I.92 Hydrogen bonds: F:W.3 ACY.40: 7 residues within 4Å: Chain F: Q.81, R.102, V.103, L.104, L.109, Y.135, E.136 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:L.109, F:E.136 Hydrogen bonds: F:Q.81, F:L.104

15 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 1 residues within 4Å: Chain A: S.5 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:S.5, H2O.1, H2O.1, H2O.4, H2O.5, H2O.6 MG.8: 1 residues within 4Å: Chain A: D.93 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.93, H2O.2, H2O.3, H2O.4, H2O.5 MG.9: 1 residues within 4Å: Chain A: N.9 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Chain B: N.9 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Chain B: S.5 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.5, H2O.7, H2O.8, H2O.11 MG.21: 1 residues within 4Å: Chain C: S.5 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:S.5, H2O.13, H2O.13, H2O.16, H2O.17, H2O.18 MG.22: 1 residues within 4Å: Chain C: D.93 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.93, H2O.14, H2O.15, H2O.16, H2O.17 MG.23: 1 residues within 4Å: Chain C: N.9 No protein-ligand interaction detected (PLIP) MG.27: 1 residues within 4Å: Chain D: N.9 No protein-ligand interaction detected (PLIP) MG.28: 1 residues within 4Å: Chain D: S.5 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:S.5, H2O.19, H2O.19, H2O.22 MG.35: 1 residues within 4Å: Chain E: S.5 6 PLIP interactions: 1 interactions with chain E, 5 Ligand-Water interactions Metal complexes: E:S.5, H2O.25, H2O.25, H2O.28, H2O.28, H2O.30 MG.36: 1 residues within 4Å: Chain E: D.93 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:D.93, H2O.25, H2O.26, H2O.28, H2O.28 MG.37: 1 residues within 4Å: Chain E: N.9 No protein-ligand interaction detected (PLIP) MG.41: 1 residues within 4Å: Chain F: N.9 No protein-ligand interaction detected (PLIP) MG.42: 1 residues within 4Å: Chain F: S.5 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:S.5, H2O.31, H2O.31, H2O.34

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hatakeyama, T. et al., Mannose oligosaccharide recognition of CGL1, a mannose-specific lectin containing DM9 motifs from Crassostrea gigas, revealed by X-ray crystallographic analysis. J.Biochem. (2023)

Release Date

2023-10-25

Peptides

Natterin-3: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
B

D
A

E
B

F
A

Natterin-3

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