SMTL ID : 3wmq.1

Crystal structure of the complex between SLL-2 and GalNAc.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-hexamer

Ligands

6 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 8 residues within 4Å: Chain A: N.60, S.62, D.64, H.74, N.76, W.78 Chain B: R.16 Ligands: CL.7 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.64 NAG-NAG.10: 8 residues within 4Å: Chain B: N.60, S.62, D.64, H.74, N.76, W.78 Chain C: R.16 Ligands: CL.16 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 8 residues within 4Å: Chain A: R.16 Chain C: N.60, S.62, D.64, H.74, N.76, W.78 Ligands: CL.25 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 8 residues within 4Å: Chain D: N.60, S.62, D.64, H.74, N.76, W.78 Chain E: R.16 Ligands: CL.34 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 8 residues within 4Å: Chain E: N.60, S.62, D.64, H.74, N.76, W.78 Chain F: R.16 Ligands: CL.43 1 PLIP interactions: 1 interactions with chain E Water bridges: E:D.64 NAG-NAG.46: 8 residues within 4Å: Chain D: R.16 Chain F: N.60, S.62, D.64, H.74, N.76, W.78 Ligands: CL.52 1 PLIP interactions: 1 interactions with chain F Water bridges: F:D.64

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

A2G.2: 9 residues within 4Å: Chain A: N.56, R.58, W.78, Y.79 Chain B: W.18, D.50, W.84 Ligands: MPD.3, CL.17 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Water bridges: B:W.18, B:N.85, A:Y.79 Hydrogen bonds: A:N.56, A:R.58, A:W.78 Salt bridges: A:R.58 A2G.11: 9 residues within 4Å: Chain B: N.56, R.58, W.78, Y.79 Chain C: W.18, D.50, W.84 Ligands: MPD.12, CL.26 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain B Water bridges: C:W.18, C:N.85, B:Y.79 Hydrogen bonds: B:N.56, B:R.58, B:W.78 Salt bridges: B:R.58 A2G.20: 9 residues within 4Å: Chain A: W.18, D.50, W.84 Chain C: N.56, R.58, W.78, Y.79 Ligands: CL.8, MPD.21 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:N.56, C:R.58, C:W.78 Water bridges: C:Y.79, A:W.18, A:N.85 Salt bridges: C:R.58 A2G.29: 9 residues within 4Å: Chain D: N.56, R.58, W.78, Y.79 Chain E: W.18, D.50, W.84 Ligands: MPD.30, CL.44 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:N.56, D:R.58, D:W.78 Water bridges: D:Y.79, E:W.18, E:N.85 Salt bridges: D:R.58 A2G.38: 9 residues within 4Å: Chain E: N.56, R.58, W.78, Y.79 Chain F: W.18, D.50, W.84 Ligands: MPD.39, CL.53 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:N.56, E:R.58, E:W.78 Water bridges: E:Y.79, F:W.18, F:N.85 Salt bridges: E:R.58 A2G.47: 9 residues within 4Å: Chain D: W.18, D.50, W.84 Chain F: N.56, R.58, W.78, Y.79 Ligands: CL.35, MPD.48 7 PLIP interactions: 5 interactions with chain F, 2 interactions with chain D Hydrogen bonds: F:N.56, F:R.58, F:W.78 Water bridges: F:Y.79, D:W.18, D:N.85 Salt bridges: F:R.58

12 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 6 residues within 4Å: Chain A: R.58, Y.79 Chain B: W.18, W.84 Ligands: A2G.2, CL.5 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.18, B:W.84, A:Y.79 MPD.4: 2 residues within 4Å: Chain B: W.18 Ligands: CL.17 No protein-ligand interaction detected (PLIP) MPD.12: 6 residues within 4Å: Chain B: R.58, Y.79 Chain C: W.18, W.84 Ligands: A2G.11, CL.14 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:W.18, C:W.84, B:Y.79 MPD.13: 2 residues within 4Å: Chain C: W.18 Ligands: CL.26 No protein-ligand interaction detected (PLIP) MPD.21: 6 residues within 4Å: Chain A: W.18, W.84 Chain C: R.58, Y.79 Ligands: A2G.20, CL.23 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:W.18, A:W.84, C:Y.79 MPD.22: 2 residues within 4Å: Chain A: W.18 Ligands: CL.8 No protein-ligand interaction detected (PLIP) MPD.30: 6 residues within 4Å: Chain D: R.58, Y.79 Chain E: W.18, W.84 Ligands: A2G.29, CL.32 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:W.18, E:W.84, D:Y.79 MPD.31: 2 residues within 4Å: Chain E: W.18 Ligands: CL.44 No protein-ligand interaction detected (PLIP) MPD.39: 6 residues within 4Å: Chain E: R.58, Y.79 Chain F: W.18, W.84 Ligands: A2G.38, CL.41 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:W.18, F:W.84, E:Y.79 MPD.40: 2 residues within 4Å: Chain F: W.18 Ligands: CL.53 No protein-ligand interaction detected (PLIP) MPD.48: 6 residues within 4Å: Chain D: W.18, W.84 Chain F: R.58, Y.79 Ligands: A2G.47, CL.50 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: F:Y.79, D:W.18, D:W.84 MPD.49: 2 residues within 4Å: Chain D: W.18 Ligands: CL.35 No protein-ligand interaction detected (PLIP)

24 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 5 residues within 4Å: Chain A: N.55, N.56, R.58, T.80 Ligands: MPD.3 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: R.7, F.36, E.37 Chain C: H.4 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain B: R.16, M.48 Ligands: NAG-NAG.1 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: W.18 Ligands: A2G.20, MPD.22 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain B: N.55, N.56, R.58, T.80 Ligands: MPD.12 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain A: H.4 Chain B: R.7, F.36, E.37 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain C: R.16, M.48 Ligands: NAG-NAG.10 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain B: W.18 Ligands: A2G.2, MPD.4 Ligand excluded by PLIP CL.23: 5 residues within 4Å: Chain C: N.55, N.56, R.58, T.80 Ligands: MPD.21 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain B: H.4 Chain C: R.7, F.36, E.37 Ligand excluded by PLIP CL.25: 3 residues within 4Å: Chain A: R.16, M.48 Ligands: NAG-NAG.19 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain C: W.18 Ligands: A2G.11, MPD.13 Ligand excluded by PLIP CL.32: 5 residues within 4Å: Chain D: N.55, N.56, R.58, T.80 Ligands: MPD.30 Ligand excluded by PLIP CL.33: 4 residues within 4Å: Chain D: R.7, F.36, E.37 Chain F: H.4 Ligand excluded by PLIP CL.34: 3 residues within 4Å: Chain E: R.16, M.48 Ligands: NAG-NAG.28 Ligand excluded by PLIP CL.35: 3 residues within 4Å: Chain D: W.18 Ligands: A2G.47, MPD.49 Ligand excluded by PLIP CL.41: 5 residues within 4Å: Chain E: N.55, N.56, R.58, T.80 Ligands: MPD.39 Ligand excluded by PLIP CL.42: 4 residues within 4Å: Chain D: H.4 Chain E: R.7, F.36, E.37 Ligand excluded by PLIP CL.43: 3 residues within 4Å: Chain F: R.16, M.48 Ligands: NAG-NAG.37 Ligand excluded by PLIP CL.44: 3 residues within 4Å: Chain E: W.18 Ligands: A2G.29, MPD.31 Ligand excluded by PLIP CL.50: 5 residues within 4Å: Chain F: N.55, N.56, R.58, T.80 Ligands: MPD.48 Ligand excluded by PLIP CL.51: 4 residues within 4Å: Chain E: H.4 Chain F: R.7, F.36, E.37 Ligand excluded by PLIP CL.52: 3 residues within 4Å: Chain D: R.16, M.48 Ligands: NAG-NAG.46 Ligand excluded by PLIP CL.53: 3 residues within 4Å: Chain F: W.18 Ligands: A2G.38, MPD.40 Ligand excluded by PLIP

6 x NA: SODIUM ION(Non-functional Binders)

NA.9: 4 residues within 4Å: Chain A: H.15, C.17, C.22, D.23 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.15, A:D.23 Water bridges: A:D.23, A:S.26, A:Y.86 NA.18: 4 residues within 4Å: Chain B: H.15, C.17, C.22, D.23 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.15, B:D.23 Water bridges: B:D.23, B:D.23 NA.27: 4 residues within 4Å: Chain C: H.15, C.17, C.22, D.23 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.15, C:D.23 NA.36: 4 residues within 4Å: Chain D: H.15, C.17, C.22, D.23 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:H.15, D:D.23 Water bridges: D:D.23, D:Y.86 NA.45: 4 residues within 4Å: Chain E: H.15, C.17, C.22, D.23 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:D.23 Water bridges: E:H.15, E:H.15, E:D.23, E:Y.86 NA.54: 4 residues within 4Å: Chain F: H.15, C.17, C.22, D.23 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:H.15, F:D.23 Water bridges: F:D.23, F:D.23, F:S.25, F:S.26

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Kita, A. et al., Crystal structure of a symbiosis-related lectin from octocoral. Glycobiology (2015)

Release Date

2015-01-14

Peptides

Galactose-binding lectin: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Galactose-binding lectin

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